Deep Learning PBMC Clustering Comparison¶

Goal: Compare clustering on PBMC data in order to regress bioinformatician bias

https://eleozzr.github.io/desc/tutorial.html DESC - The goal of this tool is to automatically identify the proper number of clusters within your single cell data according to the samples biological heterogeneity

Nevertheless, the main parameter that determines the number of clusters identified is the resolution of the clustering algorithm (typically louvain or leiden). A high resolution will identify a large number of clusters and a low resolution will identify a low number of clusters.

Consequently, we will incrementally iterate over the entire range of possible resolutions and compare the results because Control and scCLEAN.

In [1]:
import desc as desc
import numpy as np
import pandas as pd
import scanpy as sc
import matplotlib
import numpy as np
import matplotlib.pyplot as plt
%matplotlib inline 
sc.set_figure_params(dpi=200, color_map = 'viridis_r')
sc.settings.verbosity = 3             # verbosity: errors (0), warnings (1), info (2), hints (3)
sc.logging.print_versions()
WARNING: If you miss a compact list, please try `print_header`!
The `sinfo` package has changed name and is now called `session_info` to become more discoverable and self-explanatory. The `sinfo` PyPI package will be kept around to avoid breaking old installs and you can downgrade to 0.3.2 if you want to use it without seeing this message. For the latest features and bug fixes, please install `session_info` instead. The usage and defaults also changed slightly, so please review the latest README at https://gitlab.com/joelostblom/session_info.
-----
anndata     0.7.8
scanpy      1.7.2
sinfo       0.3.4
-----
2f7ece400a652629565c523b34ee61b04afa385c    NA
PIL                                         8.4.0
absl                                        NA
appnope                                     0.1.2
astunparse                                  1.6.3
backcall                                    0.2.0
cached_property                             1.5.2
certifi                                     2020.06.20
cffi                                        1.15.0
charset_normalizer                          2.0.9
cycler                                      0.10.0
cython_runtime                              NA
dateutil                                    2.8.2
decorator                                   4.4.2
defusedxml                                  0.7.1
desc                                        2.1.1
dot_parser                                  NA
entrypoints                                 0.3
flatbuffers                                 NA
gast                                        NA
get_version                                 2.1
google                                      NA
h5py                                        3.1.0
idna                                        3.3
igraph                                      0.9.8
ipykernel                                   5.5.6
ipython_genutils                            0.2.0
jedi                                        0.17.2
joblib                                      1.1.0
keras                                       2.6.0
keras_preprocessing                         1.1.2
kiwisolver                                  1.3.1
legacy_api_wrap                             1.2
llvmlite                                    0.36.0
louvain                                     0.7.0
matplotlib                                  3.3.4
mpl_toolkits                                NA
natsort                                     8.0.1
numba                                       0.53.1
numexpr                                     2.8.1
numpy                                       1.19.5
opt_einsum                                  v3.3.0
packaging                                   21.3
pandas                                      1.1.5
parso                                       0.7.1
pexpect                                     4.8.0
pickleshare                                 0.7.5
pkg_resources                               NA
prompt_toolkit                              3.0.24
ptyprocess                                  0.7.0
pydot                                       1.4.2
pygments                                    2.10.0
pyparsing                                   3.0.6
pytz                                        2021.3
requests                                    2.26.0
scipy                                       1.5.4
six                                         1.15.0
sklearn                                     0.24.2
storemagic                                  NA
tables                                      3.6.1
tensorboard                                 2.6.0
tensorflow                                  2.6.2
termcolor                                   1.1.0
texttable                                   1.6.4
threadpoolctl                               3.0.0
tornado                                     6.1
traitlets                                   4.3.3
typing_extensions                           NA
urllib3                                     1.26.7
wcwidth                                     0.2.5
wrapt                                       1.12.1
zipp                                        NA
zmq                                         22.3.0
-----
IPython             7.16.2
jupyter_client      7.1.0
jupyter_core        4.9.1
notebook            6.4.6
-----
Python 3.6.13 |Anaconda, Inc.| (default, Feb 23 2021, 12:58:59) [GCC Clang 10.0.0 ]
Darwin-20.6.0-x86_64-i386-64bit
12 logical CPU cores, i386
-----
Session information updated at 2022-06-21 15:28

Control¶

In [138]:
#input the cellranger output h5ad file from alignment to the full transcriptome
adata = desc.read_h5ad('raw_files/FUll_transcriptome/Control_not_masked_filtered_feature_bc_matrix.h5ad')
adata.var_names_make_unique()
adata
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Out[138]:
AnnData object with n_obs × n_vars = 11714 × 36601
    var: 'gene_ids', 'feature_types', 'genome'
In [140]:
#perform simple, standard QC
sc.pp.filter_cells(adata, min_counts=500)
sc.pp.filter_cells(adata, min_genes=200)
sc.pp.filter_genes(adata, min_cells=3)
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
filtered out 230 cells that have less than 200 genes expressed
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
filtered out 15194 genes that are detected in less than 3 cells
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
In [142]:
mito_genes = adata.var_names.str.startswith('MT-')
# for each cell compute fraction of counts in mito genes vs. all genes
# the `.A1` is only necessary as X is sparse (to transform to a dense array after summing)
adata.obs['percent_mito'] = np.sum(
    adata[:, mito_genes].X, axis=1).A1 / np.sum(adata.X, axis=1).A1
# add the total counts per cell as observations-annotation to adata
adata.obs['n_counts'] = adata.X.sum(axis=1).A1
In [143]:
adata.obs
Out[143]:
n_counts n_genes percent_mito
AAACCCAAGAACGTGC-1 4529.0 1306 0.036211
AAACCCAAGACAGTCG-1 4158.0 1724 0.078163
AAACCCAAGGACAACC-1 5419.0 1666 0.026020
AAACCCAAGGTTTGAA-1 6235.0 1952 0.071532
AAACCCAAGTTAACGA-1 3315.0 1527 0.085370
... ... ... ...
TTTGTTGTCCACGGGT-1 10859.0 2888 0.067502
TTTGTTGTCGAGGCAA-1 1654.0 830 0.220677
TTTGTTGTCGAGTCCG-1 5177.0 1306 0.025304
TTTGTTGTCGTTCAGA-1 3541.0 1450 0.097995
TTTGTTGTCTTCGACC-1 5712.0 1604 0.034664

11484 rows × 3 columns

In [144]:
#determine the proper thresholds according to the 99% of the data
per_cell_metrics = adata.obs
quantile = pd.DataFrame()
quantile = per_cell_metrics.quantile(0.99, numeric_only=True)
quantile
Out[144]:
n_counts        18648.920000
n_genes          4176.700000
percent_mito        0.122461
Name: 0.99, dtype: float64
In [145]:
sc.pl.violin(adata, ['n_genes', 'n_counts', 'percent_mito'],jitter=0.4, multi_panel=True)
In [146]:
#filter thresholds from 99% 
adata = adata[adata.obs['n_counts'] < 18648.92, :]
adata
Out[146]:
View of AnnData object with n_obs × n_vars = 11369 × 21407
    obs: 'n_counts', 'n_genes', 'percent_mito'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells'
In [147]:
desc.normalize_per_cell(adata, counts_per_cell_after=1e4)
normalizing by total count per cell
Trying to set attribute `.obs` of view, copying.
    finished (0:00:00): normalized adata.X and added    'n_counts', counts per cell before normalization (adata.obs)
In [148]:
desc.log1p(adata)
In [149]:
adata.raw=adata
In [150]:
sc.pp.highly_variable_genes(adata, min_mean=0.0125, max_mean=3, min_disp=0.5, subset=True)
extracting highly variable genes
    finished (0:00:00)
--> added
    'highly_variable', boolean vector (adata.var)
    'means', float vector (adata.var)
    'dispersions', float vector (adata.var)
    'dispersions_norm', float vector (adata.var)
In [151]:
#According to DESC tutorial, recomends performing analysis on highly variable genes
adata = adata[:, adata.var['highly_variable']]
In [152]:
adata
Out[152]:
View of AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
    uns: 'log1p', 'hvg'
In [153]:
#the data has to be standardized prior to DESC
desc.scale(adata, zero_center=True, max_value=3)
/Users/jbezney/opt/anaconda3/envs/DESC/lib/python3.6/site-packages/scanpy/preprocessing/_simple.py:845: UserWarning: Revieved a view of an AnnData. Making a copy.
  view_to_actual(adata)
... as `zero_center=True`, sparse input is densified and may lead to large memory consumption
In [29]:
#loop through the deep learning model and append the total number of clusters identified
#check the total number of clusters according to the resolution with which it was identified
resolution_x = [0.1,0.2,0.4,0.6,0.8,1.0,1.2,1.4,1.6,1.8,2.0]
total_clusters = []
for value in resolution_x:
    adata = desc.train(adata, dims=[adata.shape[1], 128, 32], tol=0.001, n_neighbors=10,
                   batch_size=256, louvain_resolution=[value], do_tsne=True, learning_rate=300,
                   do_umap=True, num_Cores_tsne=4)
    df_cluster = pd.DataFrame(adata.obs['desc_'+str(value)])
    df_cluster = len(df_cluster.iloc[:,0].unique())
    total_clusters.append(df_cluster)
Start to process resolution= 0.1
The number of cpu in your computer is 12
WARNING:tensorflow:From /Users/jbezney/opt/anaconda3/envs/DESC/lib/python3.6/site-packages/desc/models/desc.py:123: The name tf.keras.backend.set_session is deprecated. Please use tf.compat.v1.keras.backend.set_session instead.

Create the directory:result_tmp to save result
Checking whether result_tmp/ae_weights.h5  exists in the directory
The file ae_weights.h5 is not exits
Pretraining the 1th layer...
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 1s 6ms/step - loss: 0.5051
Epoch 2/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4777
Epoch 3/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4559
Epoch 4/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4424
Epoch 5/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4326
Epoch 6/50
45/45 [==============================] - 0s 6ms/step - loss: 0.4241
Epoch 7/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4169
Epoch 8/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4113
Epoch 9/50
45/45 [==============================] - 0s 8ms/step - loss: 0.4064
Epoch 10/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4030
Epoch 11/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4000
Epoch 12/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3976
Epoch 13/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3955
Epoch 14/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3938
Epoch 15/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3924
Epoch 16/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3911
Epoch 17/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3900
Epoch 18/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3891
Epoch 19/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3882
Epoch 20/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3873
Epoch 21/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3866
Epoch 22/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3859
Epoch 23/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3852
Epoch 24/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3846
Epoch 25/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3842
Epoch 26/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3835
Epoch 27/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3830
Epoch 28/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3825
Epoch 29/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3819
Epoch 30/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3815
Epoch 31/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3810
Epoch 32/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3806
Epoch 33/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3800
Epoch 34/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3797
Epoch 35/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3792
Epoch 36/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3788
Epoch 37/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3784
Epoch 38/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3782
Epoch 39/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3777
Epoch 40/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3773
Epoch 41/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3770
Epoch 42/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3767
Epoch 43/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3763
Epoch 44/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3761
Epoch 45/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3758
Epoch 46/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3754
Epoch 47/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3751
Epoch 48/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3749
Epoch 49/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3746
Epoch 50/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3744
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 1s 7ms/step - loss: 0.3741
Epoch 2/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3742
Epoch 3/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3741
Epoch 4/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3740
Epoch 5/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3740
Epoch 6/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3740
Epoch 7/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3739
Epoch 8/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3741
Epoch 9/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3738
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3739
Epoch 11/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3739
Epoch 12/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3738
Epoch 13/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3737
Epoch 14/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3738
Epoch 15/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3738
Epoch 16/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3738
Epoch 17/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3737
Epoch 18/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3737
Epoch 19/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3736
Epoch 20/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3736
Epoch 21/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3736
Epoch 22/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3736
Epoch 23/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3736
Epoch 24/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3735
Epoch 25/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3736
Epoch 26/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3735
Epoch 27/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3735
Epoch 28/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3735
Epoch 29/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3733
Epoch 30/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3734
Epoch 31/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3734
Epoch 32/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3734
Epoch 33/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3732
Epoch 34/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3733
Epoch 35/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3733
Epoch 36/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3733
Epoch 37/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3732
Epoch 38/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3733
Epoch 39/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3732
Epoch 40/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 41/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 42/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 43/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3731
Epoch 44/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 45/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 46/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 47/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3730
Epoch 48/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 49/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3729
Epoch 50/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3730
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 1s 7ms/step - loss: 0.3730
Epoch 2/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3731
Epoch 3/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 4/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 5/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3730
Epoch 6/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3730
Epoch 7/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3729
Epoch 8/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3731
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 11/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 12/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 13/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3728
Epoch 14/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3729
Epoch 15/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3729
Epoch 16/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3729
Epoch 17/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 00017: early stopping
The 1th layer has been pretrained.
Pretraining the 2th layer...
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 0s 936us/step - loss: 0.3967
Epoch 2/50
45/45 [==============================] - 0s 913us/step - loss: 0.2189
Epoch 3/50
45/45 [==============================] - 0s 889us/step - loss: 0.1801
Epoch 4/50
45/45 [==============================] - 0s 888us/step - loss: 0.1613
Epoch 5/50
45/45 [==============================] - 0s 883us/step - loss: 0.1512
Epoch 6/50
45/45 [==============================] - 0s 878us/step - loss: 0.1448
Epoch 7/50
45/45 [==============================] - 0s 905us/step - loss: 0.1399
Epoch 8/50
45/45 [==============================] - 0s 937us/step - loss: 0.1374
Epoch 9/50
45/45 [==============================] - 0s 974us/step - loss: 0.1342
Epoch 10/50
45/45 [==============================] - 0s 979us/step - loss: 0.1318
Epoch 11/50
45/45 [==============================] - 0s 1ms/step - loss: 0.1307
Epoch 12/50
45/45 [==============================] - 0s 1ms/step - loss: 0.1071
Epoch 13/50
45/45 [==============================] - 0s 984us/step - loss: 0.0879
Epoch 14/50
45/45 [==============================] - 0s 980us/step - loss: 0.0861
Epoch 15/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0849
Epoch 16/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0844
Epoch 17/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0836
Epoch 18/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0824
Epoch 19/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0809
Epoch 20/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0818
Epoch 21/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0807
Epoch 22/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0799
Epoch 23/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0798
Epoch 24/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0788
Epoch 25/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0782
Epoch 26/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0772
Epoch 27/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0771
Epoch 28/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0769
Epoch 29/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0762
Epoch 30/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0753
Epoch 31/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0759
Epoch 32/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0751
Epoch 33/50
45/45 [==============================] - 0s 972us/step - loss: 0.0752
Epoch 34/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0753
Epoch 35/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0745
Epoch 36/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0739
Epoch 37/50
45/45 [==============================] - 0s 955us/step - loss: 0.0739
Epoch 38/50
45/45 [==============================] - 0s 985us/step - loss: 0.0738
Epoch 39/50
45/45 [==============================] - 0s 951us/step - loss: 0.0732
Epoch 40/50
45/45 [==============================] - 0s 928us/step - loss: 0.0726
Epoch 41/50
45/45 [==============================] - 0s 923us/step - loss: 0.0730
Epoch 42/50
45/45 [==============================] - 0s 925us/step - loss: 0.0732
Epoch 43/50
45/45 [==============================] - 0s 898us/step - loss: 0.0727
Epoch 44/50
45/45 [==============================] - 0s 926us/step - loss: 0.0719
Epoch 45/50
45/45 [==============================] - 0s 918us/step - loss: 0.0723
Epoch 46/50
45/45 [==============================] - 0s 942us/step - loss: 0.0713
Epoch 47/50
45/45 [==============================] - 0s 997us/step - loss: 0.0712
Epoch 48/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0707
Epoch 49/50
45/45 [==============================] - 0s 968us/step - loss: 0.0715
Epoch 50/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0715
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 0s 946us/step - loss: 0.0711
Epoch 2/50
45/45 [==============================] - 0s 930us/step - loss: 0.0706
Epoch 3/50
45/45 [==============================] - 0s 875us/step - loss: 0.0707
Epoch 4/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0711
Epoch 5/50
45/45 [==============================] - 0s 906us/step - loss: 0.0710
Epoch 6/50
45/45 [==============================] - 0s 932us/step - loss: 0.0710
Epoch 7/50
45/45 [==============================] - 0s 892us/step - loss: 0.0709
Epoch 8/50
45/45 [==============================] - 0s 881us/step - loss: 0.0709
Epoch 9/50
45/45 [==============================] - 0s 920us/step - loss: 0.0705
Epoch 10/50
45/45 [==============================] - 0s 938us/step - loss: 0.0699
Epoch 11/50
45/45 [==============================] - 0s 942us/step - loss: 0.0709
Epoch 12/50
45/45 [==============================] - 0s 972us/step - loss: 0.0697
Epoch 13/50
45/45 [==============================] - 0s 959us/step - loss: 0.0699
Epoch 14/50
45/45 [==============================] - 0s 991us/step - loss: 0.0701
Epoch 15/50
45/45 [==============================] - 0s 976us/step - loss: 0.0700
Epoch 16/50
45/45 [==============================] - 0s 978us/step - loss: 0.0705
Epoch 17/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0704
Epoch 18/50
45/45 [==============================] - 0s 996us/step - loss: 0.0703
Epoch 19/50
45/45 [==============================] - 0s 967us/step - loss: 0.0695
Epoch 20/50
45/45 [==============================] - 0s 960us/step - loss: 0.0706
Epoch 21/50
45/45 [==============================] - 0s 968us/step - loss: 0.0703
Epoch 22/50
45/45 [==============================] - 0s 964us/step - loss: 0.0701
Epoch 23/50
45/45 [==============================] - 0s 952us/step - loss: 0.0708
Epoch 24/50
45/45 [==============================] - 0s 988us/step - loss: 0.0703
Epoch 25/50
45/45 [==============================] - 0s 991us/step - loss: 0.0704
Epoch 26/50
45/45 [==============================] - 0s 956us/step - loss: 0.0700
Epoch 27/50
45/45 [==============================] - 0s 965us/step - loss: 0.0705
Epoch 28/50
45/45 [==============================] - 0s 983us/step - loss: 0.0705
Epoch 29/50
45/45 [==============================] - 0s 966us/step - loss: 0.0703
Epoch 00029: early stopping
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 0s 940us/step - loss: 0.0704
Epoch 2/50
45/45 [==============================] - 0s 934us/step - loss: 0.0701
Epoch 3/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0702
Epoch 4/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0706
Epoch 5/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0706
Epoch 6/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0705
Epoch 7/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0706
Epoch 8/50
45/45 [==============================] - 0s 997us/step - loss: 0.0706
Epoch 9/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0701
Epoch 10/50
45/45 [==============================] - 0s 953us/step - loss: 0.0696
Epoch 11/50
45/45 [==============================] - 0s 904us/step - loss: 0.0706
Epoch 12/50
45/45 [==============================] - 0s 887us/step - loss: 0.0693
Epoch 13/50
45/45 [==============================] - 0s 869us/step - loss: 0.0697
Epoch 14/50
45/45 [==============================] - 0s 874us/step - loss: 0.0698
Epoch 15/50
45/45 [==============================] - 0s 867us/step - loss: 0.0697
Epoch 16/50
45/45 [==============================] - 0s 900us/step - loss: 0.0703
Epoch 17/50
45/45 [==============================] - 0s 865us/step - loss: 0.0701
Epoch 18/50
45/45 [==============================] - 0s 874us/step - loss: 0.0701
Epoch 19/50
45/45 [==============================] - 0s 879us/step - loss: 0.0693
Epoch 20/50
45/45 [==============================] - 0s 881us/step - loss: 0.0704
Epoch 21/50
45/45 [==============================] - 0s 911us/step - loss: 0.0701
Epoch 22/50
45/45 [==============================] - 0s 965us/step - loss: 0.0700
Epoch 00022: early stopping
The 2th layer has been pretrained.
Copying layer-wise pretrained weights to deep autoencoders
Fine-tuning autoencoder end-to-end
learning rate = 1
Epoch 1/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3707
Epoch 2/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3694
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3686
Epoch 4/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3680
Epoch 5/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3674
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3669
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3664
Epoch 8/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3660
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3656
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3652
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3648
Epoch 12/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3644
Epoch 13/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3640
Epoch 14/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3637
Epoch 15/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3634
Epoch 16/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3630
Epoch 17/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3627
Epoch 18/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3624
Epoch 19/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3621
Epoch 20/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3619
Epoch 21/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3616
Epoch 22/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3613
Epoch 23/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3611
Epoch 24/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3608
Epoch 25/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3606
Epoch 26/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3603
Epoch 27/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3601
Epoch 28/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3599
Epoch 29/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3596
Epoch 30/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3594
Epoch 31/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3592
Epoch 32/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3590
Epoch 33/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3588
Epoch 34/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3586
Epoch 35/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3584
Epoch 36/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3582
Epoch 37/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3580
Epoch 38/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3579
Epoch 39/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3577
Epoch 40/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3575
Epoch 41/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3573
Epoch 42/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3572
Epoch 43/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3570
Epoch 44/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3568
Epoch 45/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3567
Epoch 46/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3565
Epoch 47/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3564
Epoch 48/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3562
Epoch 49/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3561
Epoch 50/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3559
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3555
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3554
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3554
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3554
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3553
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3553
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3553
Epoch 8/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3553
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3553
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3553
Epoch 11/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3553
Epoch 12/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3552
Epoch 13/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3552
Epoch 14/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3552
Epoch 15/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3552
Epoch 16/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3552
Epoch 17/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3552
Epoch 18/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3552
Epoch 19/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3551
Epoch 20/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3551
Epoch 21/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3551
Epoch 22/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3551
Epoch 23/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3551
Epoch 24/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3551
Epoch 25/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3551
Epoch 26/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3550
Epoch 27/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3550
Epoch 28/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3550
Epoch 29/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3550
Epoch 30/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3550
Epoch 31/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3550
Epoch 32/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3550
Epoch 33/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 34/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 35/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3549
Epoch 36/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 37/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 38/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 39/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 40/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 41/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 42/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 43/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 44/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 45/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 46/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 47/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 48/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 49/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 50/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 00011: early stopping
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 00011: early stopping
learning rate = 0.0001
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 00011: early stopping
learning rate = 1e-05
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 00011: early stopping
Pretraining time is 78.82858276367188
Pretrained weights are saved to result_tmp /ae_weights.h5
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:12)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 6 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.01627231946521242 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0628
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0462
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0385
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0328
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0283
The value of delta_label of current 2 th iteration is 0.029905884422552556 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1122
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0890
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0722
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0597
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0502
The value of delta_label of current 3 th iteration is 0.022605330284105902 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1294
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1037
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0858
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0732
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0640
The value of delta_label of current 4 th iteration is 0.013017855572169936 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1307
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1085
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0937
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0832
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0755
The value of delta_label of current 5 th iteration is 0.008883806843170024 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1219
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1086
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0991
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0920
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0863
The value of delta_label of current 6 th iteration is 0.007036678687659424 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1107
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1040
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0988
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0945
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0907
The value of delta_label of current 7 th iteration is 0.004573841146978626 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1026
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0987
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0953
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0924
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0898
The value of delta_label of current 8 th iteration is 0.003606297827425455 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0967
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0940
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0916
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0895
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0875
The value of delta_label of current 9 th iteration is 0.002023045122702085 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0922
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0902
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0884
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0867
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0852
The value of delta_label of current 10 th iteration is 0.0019350866391063418 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0887
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0871
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0857
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0843
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0831
The value of delta_label of current 11 th iteration is 0.001759169671914856 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0858
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0846
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0834
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0823
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0812
The value of delta_label of current 12 th iteration is 0.0014952942211276278 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0835
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0824
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0814
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0804
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0795
The value of delta_label of current 13 th iteration is 0.0021110036062978272 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0816
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0806
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0797
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0789
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0781
delta_label  0.0009675433195531709 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0    4964
1    2455
2    2454
3     776
4     548
5     172
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_2"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 6)                 192       
=================================================================
Total params: 277,344
Trainable params: 277,344
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.1)is: 104.78796601295471
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne0.1  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.1  into the umap coordinates (adata.obsm)

The run time for all resolution is: 136.38761711120605
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1'
    obsp: 'distances', 'connectivities'
Start to process resolution= 0.2
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.016122102737426758
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 9 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.03465564253672267 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0789
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0624
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0538
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0470
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0414
The value of delta_label of current 2 th iteration is 0.019614741841850646 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1356
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1126
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0948
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0811
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0704
The value of delta_label of current 3 th iteration is 0.013193772539361421 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1627
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1389
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1199
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1051
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0936
The value of delta_label of current 4 th iteration is 0.010906851965872108 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1780
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1553
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1378
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1246
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1143
The value of delta_label of current 5 th iteration is 0.012490104670595479 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1837
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1666
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1535
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1433
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1351
The value of delta_label of current 6 th iteration is 0.010818893482276366 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1804
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1696
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1608
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1535
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1473
The value of delta_label of current 7 th iteration is 0.011698478318233793 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1738
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1665
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1603
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1550
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1503
The value of delta_label of current 8 th iteration is 0.011610519834638051 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1680
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1626
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1579
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1538
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1501
The value of delta_label of current 9 th iteration is 0.011082768933063593 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1640
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1596
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1557
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1524
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1493
The value of delta_label of current 10 th iteration is 0.009763391679127452 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1612
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1574
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1540
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1510
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1483
The value of delta_label of current 11 th iteration is 0.009147682293957252 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1588
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1554
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1523
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1496
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1470
The value of delta_label of current 12 th iteration is 0.006684844753276454 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1564
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1533
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1504
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1479
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1456
The value of delta_label of current 13 th iteration is 0.005101592048553083 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1537
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1508
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1483
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1461
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1439
The value of delta_label of current 14 th iteration is 0.0034303808602339694 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1507
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1482
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1459
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1439
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1420
The value of delta_label of current 15 th iteration is 0.0021110036062978272 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1474
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1453
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1433
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1416
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1399
The value of delta_label of current 16 th iteration is 0.0015832527047233706 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1442
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1423
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1406
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1391
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1376
The value of delta_label of current 17 th iteration is 0.001407335737531885 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1411
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1395
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1380
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1367
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1354
delta_label  0.0009675433195531709 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is:
0    3383
1    2129
2    1575
3    1619
4     773
5     419
6     317
7     147
8    1007
dtype: int64
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_3"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 9)                 288       
=================================================================
Total params: 277,440
Trainable params: 277,440
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.2)is: 16.52006721496582
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.2  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.2  into the umap coordinates (adata.obsm)

The run time for all resolution is: 47.07176899909973
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2'
    obsp: 'distances', 'connectivities'
Start to process resolution= 0.4
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.017837047576904297
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 9 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.032456680446829096 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0789
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0624
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0539
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0470
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0414
The value of delta_label of current 2 th iteration is 0.01970270032544639 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1355
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1126
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0948
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0811
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0704
The value of delta_label of current 3 th iteration is 0.012578063154191221 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1624
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1387A: 0s - loss: 0.14
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1198
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1050
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0936
The value of delta_label of current 4 th iteration is 0.011434602867446565 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1775
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1549
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1375
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1244
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1141
The value of delta_label of current 5 th iteration is 0.012402146186999736 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1833
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1662
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1531
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1430
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1348
The value of delta_label of current 6 th iteration is 0.011962353769021022 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1805
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1696
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1607
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1534
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1472
The value of delta_label of current 7 th iteration is 0.011786436801829536 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1742
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1668
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1606
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1552
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1505
The value of delta_label of current 8 th iteration is 0.012050312252616765 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1685
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1630
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1583
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1542
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1504
The value of delta_label of current 9 th iteration is 0.01125868590025508 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1645
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1601
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1561
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1528
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1496
The value of delta_label of current 10 th iteration is 0.01064297651508488 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1617
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1578
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1544
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1514
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1486
The value of delta_label of current 11 th iteration is 0.008004222007212595 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1593
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1558
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1527
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1500
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1475
The value of delta_label of current 12 th iteration is 0.006508927786084968 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1568
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1536
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1508
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1483
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1460
The value of delta_label of current 13 th iteration is 0.005365467499340312 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1541
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1511
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1486
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1463
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1442
The value of delta_label of current 14 th iteration is 0.0038701732782126835 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1511
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1484
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1462
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1442
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1423
The value of delta_label of current 15 th iteration is 0.00219896208989357 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1479
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1456
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1437
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1419
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1402
The value of delta_label of current 16 th iteration is 0.0015832527047233706 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1446
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1427
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1411
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1395
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1380
The value of delta_label of current 17 th iteration is 0.0015832527047233706 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1415
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1399
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1384
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1371
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1358
delta_label  0.000439792417978714 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0    3358
1    2129
2    1577
3    1636
4     773
5     419
6     316
7     147
8    1014
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_4"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 9)                 288       
=================================================================
Total params: 277,440
Trainable params: 277,440
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.4)is: 16.41282367706299
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.4  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.4  into the umap coordinates (adata.obsm)

The run time for all resolution is: 47.394776821136475
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4'
    obsp: 'distances', 'connectivities'
Start to process resolution= 0.6
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.013768911361694336
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 10 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.06420969302489225 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0842
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0677
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0592
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0522
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0464
The value of delta_label of current 2 th iteration is 0.025507960242765415 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1465
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1233
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1050
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0905
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0788
The value of delta_label of current 3 th iteration is 0.01345764799014865 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1808
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1548
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1337
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1173
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1043
The value of delta_label of current 4 th iteration is 0.01222622921980825 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2038
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1779
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1582
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1433
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1318
The value of delta_label of current 5 th iteration is 0.010555018031489137 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2164
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1975
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1831
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1719
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1628
The value of delta_label of current 6 th iteration is 0.009147682293957252 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2167
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2048
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1949
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1866
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1795
The value of delta_label of current 7 th iteration is 0.007388512622042396 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2104
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2023
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1951
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1888
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1832
The value of delta_label of current 8 th iteration is 0.004485882663382883 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2030
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1969
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1912
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1863
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1818
The value of delta_label of current 9 th iteration is 0.0037822147946169407 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1958
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1909
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1863
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1822
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1784
The value of delta_label of current 10 th iteration is 0.0029026299586595128 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1891
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1850
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1812
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1777
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1745
The value of delta_label of current 11 th iteration is 0.0012314187703403993 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1828
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1794
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1762
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1733
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1706
The value of delta_label of current 12 th iteration is 0.001407335737531885 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1770
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1742
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1715
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1690
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1667
delta_label  0.0007916263523616853 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0    2402
1    2081
2    2179
3    1578
4    1365
5     779
6     396
7     315
8     192
9      82
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_5"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 10)                320       
=================================================================
Total params: 277,472
Trainable params: 277,472
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.6)is: 13.11959195137024
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.6  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.6  into the umap coordinates (adata.obsm)

The run time for all resolution is: 43.96219491958618
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6'
    obsp: 'distances', 'connectivities'
Start to process resolution= 0.8
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.014747142791748047
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 11 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.052159380772275485 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0894
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0730
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0641
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0568
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0507
The value of delta_label of current 2 th iteration is 0.021110036062978274 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1482
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1251
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1071
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0931
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0821
The value of delta_label of current 3 th iteration is 0.010906851965872108 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1813
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1565
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1367
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1210
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1086
The value of delta_label of current 4 th iteration is 0.011082768933063593 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2061
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1810
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1621
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1479
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1368
The value of delta_label of current 5 th iteration is 0.008883806843170024 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2221
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2034
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1891
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1779
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1687
The value of delta_label of current 6 th iteration is 0.008531972908787053 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2239
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2119
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2020
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1936
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1864
The value of delta_label of current 7 th iteration is 0.0063330108188934826 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2186
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2101
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2027
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1961
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1902
The value of delta_label of current 8 th iteration is 0.005189550532148826 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2114
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2048
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1990
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1937
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1889
The value of delta_label of current 9 th iteration is 0.0031665054094467413 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2041
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1988
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1940
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1897
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1857
The value of delta_label of current 10 th iteration is 0.0024628375406807986 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1972
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1928
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1888
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1852
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1818
The value of delta_label of current 11 th iteration is 0.0015832527047233706 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1907
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1871
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1837
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1807
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1778
The value of delta_label of current 12 th iteration is 0.0013193772539361421 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1848
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1817
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1790
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1764
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1739
The value of delta_label of current 13 th iteration is 0.0010555018031489136 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1794
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1768
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1745
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1723
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1702
delta_label  0.0006157093851701996 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0     2487
1     2235
2     2137
3     1576
4     1252
5      446
6      393
7      331
8      318
9      138
10      56
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_6"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 11)                352       
=================================================================
Total params: 277,504
Trainable params: 277,504
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.8)is: 13.096119165420532
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.8  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.8  into the umap coordinates (adata.obsm)

The run time for all resolution is: 43.638885736465454
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8'
    obsp: 'distances', 'connectivities'
Start to process resolution= 1.0
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.014670133590698242
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 13 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.06711232298355177 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0996
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0831
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0737
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0660
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0594
The value of delta_label of current 2 th iteration is 0.03632685372504178 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1611
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1407
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1239
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1101
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0988
The value of delta_label of current 3 th iteration is 0.03131322016008444 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1978
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1753
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1568
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1418
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1296
The value of delta_label of current 4 th iteration is 0.031137303192892953 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2302
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2054
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1866
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1721
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1608
The value of delta_label of current 5 th iteration is 0.023836749054446302 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2515
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2322
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2176
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2060
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1965
The value of delta_label of current 6 th iteration is 0.017679655202744303 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2582
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2451
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2345
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2254
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2176
The value of delta_label of current 7 th iteration is 0.01064297651508488 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2574
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2478
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2397
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2324
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2260
The value of delta_label of current 8 th iteration is 0.008619931392382795 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2533
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2459
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2393
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2331
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2276
The value of delta_label of current 9 th iteration is 0.0047497581141701115 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2480
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2416
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2358
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2303
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2254
The value of delta_label of current 10 th iteration is 0.0038701732782126835 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2422
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2367
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2318
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2270
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2228
The value of delta_label of current 11 th iteration is 0.0030785469258509984 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2361
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2314
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2271
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2230
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2193
The value of delta_label of current 12 th iteration is 0.00219896208989357 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2298
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2257
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2220
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2185
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2153
The value of delta_label of current 13 th iteration is 0.0010555018031489136 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2237
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2202
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2171
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2141
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2113
delta_label  0.0007916263523616853 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0     2364
1     2153
2     1564
3     1259
4      467
5      962
6      444
7      390
8     1012
9      333
10     278
11      96
12      47
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_7"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 13)                416       
=================================================================
Total params: 277,568
Trainable params: 277,568
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=1.0)is: 13.499810934066772
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne1.0  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.0  into the umap coordinates (adata.obsm)

The run time for all resolution is: 44.50366282463074
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0'
    obsp: 'distances', 'connectivities'
Start to process resolution= 1.2
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.018655061721801758
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 13 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.06632069663119008 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0996
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0831
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0738
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0661
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0595
The value of delta_label of current 2 th iteration is 0.03606297827425455 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1608
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1406
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1238
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1101
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0987
The value of delta_label of current 3 th iteration is 0.029817925938956814 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1976
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1749
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1563
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1412
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1291
The value of delta_label of current 4 th iteration is 0.031840971061658896 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2303
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2052
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1863
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1718
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1605
The value of delta_label of current 5 th iteration is 0.024892250857595215 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2516
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2322
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2176
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2060
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1965
The value of delta_label of current 6 th iteration is 0.015744568563637963 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2580
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2449
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2343
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2252
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2174
The value of delta_label of current 7 th iteration is 0.011170727416659337 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2569
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2475
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2395
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2321
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2258
The value of delta_label of current 8 th iteration is 0.007652388072829625 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2529
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2455
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2390
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2329
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2274
The value of delta_label of current 9 th iteration is 0.00562934295012754 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2476
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2413
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2356
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2302
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2252
The value of delta_label of current 10 th iteration is 0.00439792417978714 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2418
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2363
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2314
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2267
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2224
The value of delta_label of current 11 th iteration is 0.0034303808602339694 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2358
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2311
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2269
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2228
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2190
The value of delta_label of current 12 th iteration is 0.002023045122702085 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2296
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2256
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2219
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2183
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2150
The value of delta_label of current 13 th iteration is 0.001759169671914856 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2236
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2201
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2169
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2139
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2110
The value of delta_label of current 14 th iteration is 0.0011434602867446565 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2179
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2149
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2121
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2096
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2071
delta_label  0.0002638754507872284 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0     2357
1     2163
2     1564
3     1258
4      464
5      963
6      444
7      390
8     1017
9      333
10     278
11      42
12      96
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_8"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 13)                416       
=================================================================
Total params: 277,568
Trainable params: 277,568
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=1.2)is: 14.362415790557861
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:31)
computing neighbors
tsne finished and added X_tsne1.2  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.2  into the umap coordinates (adata.obsm)

The run time for all resolution is: 46.85865616798401
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2'
    obsp: 'distances', 'connectivities'
Start to process resolution= 1.4
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.016456127166748047
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 15 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.07590817134312604 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1028
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0867
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0775
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0701
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0638
The value of delta_label of current 2 th iteration is 0.04116457032280763 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1653
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1461
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1301
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1168
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1057
The value of delta_label of current 3 th iteration is 0.03606297827425455 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2046
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1822
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1640
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1495
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1377
The value of delta_label of current 4 th iteration is 0.03773418946257367 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2424
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2182
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1997
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1854
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1741
The value of delta_label of current 5 th iteration is 0.029905884422552556 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2701
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2508
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2360
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2242
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2144
The value of delta_label of current 6 th iteration is 0.02251737180051016 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2805
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2671
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2562
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2470
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2389
The value of delta_label of current 7 th iteration is 0.014864983727680536 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2824
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2725
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2639
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2564
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2496
The value of delta_label of current 8 th iteration is 0.009323599261148738 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2810
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2732
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2661
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2598
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2540
The value of delta_label of current 9 th iteration is 0.010115225613510423 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2781
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2715
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2655
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2599
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2548
The value of delta_label of current 10 th iteration is 0.006772803236872196 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2744
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2687
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2633
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2584
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2538
The value of delta_label of current 11 th iteration is 0.0058052599173190255 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2702
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2651
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2603
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2559
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2517
The value of delta_label of current 12 th iteration is 0.003958131761808426 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2655
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2610
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2566
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2526
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2488
The value of delta_label of current 13 th iteration is 0.0029905884422552556 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2604
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2564
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2525
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2489
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2454
The value of delta_label of current 14 th iteration is 0.003342422376638227 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2551
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2516
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2481
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2449
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2417
The value of delta_label of current 15 th iteration is 0.002023045122702085 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2500
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2469
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2437
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2408
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2379
The value of delta_label of current 16 th iteration is 0.0014952942211276278 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2450
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2421
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2392
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2366
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2340
delta_label  0.0009675433195531709 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is:
0     2349
1     1666
2     1563
3     1168
4      352
5      884
6      444
7      388
8      978
9      334
10     283
11      47
12      94
13     162
14     657
dtype: int64
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_9"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 15)                480       
=================================================================
Total params: 277,632
Trainable params: 277,632
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=1.4)is: 17.228896141052246
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne1.4  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.4  into the umap coordinates (adata.obsm)

The run time for all resolution is: 48.980205059051514
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4'
    obsp: 'distances', 'connectivities'
Start to process resolution= 1.6
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.01580333709716797
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 17 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.10255959187263612 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1060
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0897
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0807
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0733
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0670
The value of delta_label of current 2 th iteration is 0.05602955405048817 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1711
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1519
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1359
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1227
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1115
The value of delta_label of current 3 th iteration is 0.04565045298619052 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2100
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1889
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1716
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1574
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1455
The value of delta_label of current 4 th iteration is 0.043275573929105464 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2445
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2229
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2060
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1928
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1820
The value of delta_label of current 5 th iteration is 0.03703052159380772 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2727
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2549
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2409
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2297
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2202
The value of delta_label of current 6 th iteration is 0.033776057700765236 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2874
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2741
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2632
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2540
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2459
The value of delta_label of current 7 th iteration is 0.026563462045914327 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2929
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2827
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2739
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2662
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2592
The value of delta_label of current 8 th iteration is 0.01917494942387193 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2940
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2857
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2784
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2716
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2654
The value of delta_label of current 9 th iteration is 0.016975987333978364 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2928
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2856
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2792
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2733
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2678
The value of delta_label of current 10 th iteration is 0.015568651596446477 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2902
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2840
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2783
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2730
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2681
The value of delta_label of current 11 th iteration is 0.011346644383850822 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2871
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2816
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2765
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2717
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2673
The value of delta_label of current 12 th iteration is 0.00905972381036151 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2843
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2792
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2746
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2702
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2662
The value of delta_label of current 13 th iteration is 0.0050136335649573404 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2819
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2772
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2730
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2689
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2653
The value of delta_label of current 14 th iteration is 0.003606297827425455 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2795
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2752
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2713
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2675
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2642
The value of delta_label of current 15 th iteration is 0.0025507960242765414 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2768
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2728
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2692
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2658
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2627
The value of delta_label of current 16 th iteration is 0.001847128155510599 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2734
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2698
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2666
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2634
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2606
The value of delta_label of current 17 th iteration is 0.0021110036062978272 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2696
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2663
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2634
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2606
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2580
The value of delta_label of current 18 th iteration is 0.0013193772539361421 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2655
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2625
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2600
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2574
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2550
delta_label  0.0002638754507872284 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is:
0     2170
1     1272
2     1149
3     1231
4      418
5      895
6     1132
7      445
8      386
9      996
10     334
11     285
12     359
13      27
14     173
15      82
16      15
dtype: int64
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_10"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 17)                544       
=================================================================
Total params: 277,696
Trainable params: 277,696
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=1.6)is: 19.20682692527771
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne1.6  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.6  into the umap coordinates (adata.obsm)

The run time for all resolution is: 51.01515197753906
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6'
    obsp: 'distances', 'connectivities'
Start to process resolution= 1.8
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.012847185134887695
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 20 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.1493535051455713 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1115
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0957
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0870
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0797
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0735
The value of delta_label of current 2 th iteration is 0.07370920925323247 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1770
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1593
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1441
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1312
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1201
The value of delta_label of current 3 th iteration is 0.055237927698126486 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2174
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1973
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1808
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1673
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1560
The value of delta_label of current 4 th iteration is 0.052687131673849946 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2551
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2348
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2184
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2052
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1946
The value of delta_label of current 5 th iteration is 0.060075644295892336 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2857
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2688
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2551
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2437
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2343
The value of delta_label of current 6 th iteration is 0.057524848271615796 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3016
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2888
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2780
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2686
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2605
The value of delta_label of current 7 th iteration is 0.04653003782214794 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3073
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2972
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2884
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2804
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2732
The value of delta_label of current 8 th iteration is 0.031577095610871665 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3075
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2991
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2915
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2845
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2781
The value of delta_label of current 9 th iteration is 0.024276541472425014 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3047
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2974
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2910
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2848
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2793
The value of delta_label of current 10 th iteration is 0.021725745448148474 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3001
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2939
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2883
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2828
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2780
The value of delta_label of current 11 th iteration is 0.01996657577623362 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2948
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2893
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2844
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2796
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2753
The value of delta_label of current 12 th iteration is 0.021813703931744217 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2891
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2844
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2801
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2759
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2721
The value of delta_label of current 13 th iteration is 0.01882311548948896 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2836
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2795
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2757
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2720
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2686
The value of delta_label of current 14 th iteration is 0.016360277948808163 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2785
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2748
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2714
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2682
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2652
The value of delta_label of current 15 th iteration is 0.017415779751957076 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2738
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2705
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2676
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2647
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2621
The value of delta_label of current 16 th iteration is 0.015392734629254992 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2696
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2667
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2641
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2616
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2592
The value of delta_label of current 17 th iteration is 0.013985398891723106 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2660
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2634
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2610
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2588
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2566
The value of delta_label of current 18 th iteration is 0.01345764799014865 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2629
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2606
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2584
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2564
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2544
The value of delta_label of current 19 th iteration is 0.012666021637786965 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2602
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2582
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2562
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2543
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2525
The value of delta_label of current 20 th iteration is 0.01187439528542528 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2579
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2561
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2543
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2525
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2509
The value of delta_label of current 21 th iteration is 0.012402146186999736 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2560
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2543
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2526
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2511
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2496
The value of delta_label of current 22 th iteration is 0.01222622921980825 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2544
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2528
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2513
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2498
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2484
The value of delta_label of current 23 th iteration is 0.009587474711935965 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2532
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2517
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2502
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2489
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2476
The value of delta_label of current 24 th iteration is 0.009323599261148738 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2523
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2508
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2495
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2482
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2470
The value of delta_label of current 25 th iteration is 0.00782830504002111 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2517
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2504
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2490
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2478
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2466
The value of delta_label of current 26 th iteration is 0.007388512622042396 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2515
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2501
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2489
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2477
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2466
The value of delta_label of current 27 th iteration is 0.0063330108188934826 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2514
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2501
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2489
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2477
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2466
The value of delta_label of current 28 th iteration is 0.005717301433723282 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2513
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2500
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2488
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2477
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2467
The value of delta_label of current 29 th iteration is 0.0047497581141701115 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2511
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2499
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2487
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2476
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2466
The value of delta_label of current 30 th iteration is 0.0031665054094467413 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2507
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2495
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2484
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2473
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2463
The value of delta_label of current 31 th iteration is 0.003606297827425455 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2501
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2490
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2479
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2468
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2458
The value of delta_label of current 32 th iteration is 0.0021110036062978272 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2493
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2482
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2471
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2461
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2451
The value of delta_label of current 33 th iteration is 0.00219896208989357 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2482
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2472
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2461
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2451
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2442
The value of delta_label of current 34 th iteration is 0.0023748790570850557 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2469
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2459
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2449
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2440
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2431
The value of delta_label of current 35 th iteration is 0.0016712111883191135 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2454
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2445
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2435
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2427
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2418
The value of delta_label of current 36 th iteration is 0.001407335737531885 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2438
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2430
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2421
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2413
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2405
The value of delta_label of current 37 th iteration is 0.0014952942211276278 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2422
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2414
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2406
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2398
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2391
The value of delta_label of current 38 th iteration is 0.0014952942211276278 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2406
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2398
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2391
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2384
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2377
The value of delta_label of current 39 th iteration is 0.0031665054094467413 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2390
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2383
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2377
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2370
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2364
The value of delta_label of current 40 th iteration is 0.0034303808602339694 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2375
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2369
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2363
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2357
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2352
The value of delta_label of current 41 th iteration is 0.003958131761808426 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2361
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2355
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2350
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2344
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2339
The value of delta_label of current 42 th iteration is 0.004309965696191398 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2348
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2342
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2337
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2332
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2327
The value of delta_label of current 43 th iteration is 0.003694256311021198 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2335
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2330
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2325
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2320
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2316
The value of delta_label of current 44 th iteration is 0.002286920573489313 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2322
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2318
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2313
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2309
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2304
The value of delta_label of current 45 th iteration is 0.002726712991468027 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2310
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2306
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2302
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2297
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2293
The value of delta_label of current 46 th iteration is 0.003342422376638227 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2299
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2295
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2290
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2286
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2282
The value of delta_label of current 47 th iteration is 0.002023045122702085 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2287
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2283
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2279
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2275
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2271
The value of delta_label of current 48 th iteration is 0.002286920573489313 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2276
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2272
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2269
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2265
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2261
The value of delta_label of current 49 th iteration is 0.00219896208989357 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2265
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2262
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2258
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2254
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2251
The value of delta_label of current 50 th iteration is 0.0029905884422552556 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2255
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2252
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2248
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2245
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2242
The value of delta_label of current 51 th iteration is 0.00439792417978714 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2245
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2242
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2239
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2236
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2233
The value of delta_label of current 52 th iteration is 0.008883806843170024 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 4ms/step - loss: 0.2236
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2233
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2230
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2227
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2224
The value of delta_label of current 53 th iteration is 0.008180138974404082 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2227
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2224
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2222
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2219
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2216
The value of delta_label of current 54 th iteration is 0.013809481924531622 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2219
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2216
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2213
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2211
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2208
The value of delta_label of current 55 th iteration is 0.017063945817574106 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2210
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2208
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2205
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2203
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2200
The value of delta_label of current 56 th iteration is 0.024892250857595215 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2202
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2200
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2198
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2195
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2192
The value of delta_label of current 57 th iteration is 0.028234673234233443 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2195
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2192
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2190
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2187
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2185
The value of delta_label of current 58 th iteration is 0.035007476471105636 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2187
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2185
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2182
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2180
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2178
The value of delta_label of current 59 th iteration is 0.03386401618436098 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2179
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2177
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2175
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2173
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2171
The value of delta_label of current 60 th iteration is 0.03465564253672267 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2172
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2170
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2168
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2166
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2164
The value of delta_label of current 61 th iteration is 0.027970797783446213 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2165
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2163
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2161
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2159
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2157
The value of delta_label of current 62 th iteration is 0.020494326677808074 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2158
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2157
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2155
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2153
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2150
The value of delta_label of current 63 th iteration is 0.018031489137127276 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2152
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2150
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2148
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2146
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2144
The value of delta_label of current 64 th iteration is 0.02128595303016976 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2145
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2144
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2142
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2140
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2138
The value of delta_label of current 65 th iteration is 0.017327821268361333 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2139
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2138
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2136
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2134
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2132
The value of delta_label of current 66 th iteration is 0.00782830504002111 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2133
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2132
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2130
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2128
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2127
The value of delta_label of current 67 th iteration is 0.007740346556425367 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2128
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2126
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2125
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2123
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2121
The value of delta_label of current 68 th iteration is 0.004573841146978626 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2122
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2121
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2119
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2118
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2116
delta_label  0.0 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0     2234
1      857
2     1206
3     1251
4     1464
5      799
6      466
7      346
8      445
9       17
10     381
11     634
12     333
13     378
14     281
15      23
16     156
17      83
18      15
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_11"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 20)                640       
=================================================================
Total params: 277,792
Trainable params: 277,792
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=1.8)is: 66.3656268119812
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:32)
computing neighbors
tsne finished and added X_tsne1.8  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.8  into the umap coordinates (adata.obsm)

The run time for all resolution is: 99.36555004119873
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6', 'desc_1.8'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6', 'prob_matrix1.8'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6', 'X_Embeded_z1.8', 'X_tsne1.8', 'X_umap1.8'
    obsp: 'distances', 'connectivities'
Start to process resolution= 2.0
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.014740943908691406
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 24 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.19905004837716597 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1131
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0982
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0899
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0831
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0772
The value of delta_label of current 2 th iteration is 0.08039405400650892 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1790
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1629
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1491
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1372
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1272
The value of delta_label of current 3 th iteration is 0.06139502154982848 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2189
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2021
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1876
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1754
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1650
The value of delta_label of current 4 th iteration is 0.05866830855836045 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2540
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2362
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2214
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2093
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1992
The value of delta_label of current 5 th iteration is 0.06693640601636028 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 4ms/step - loss: 0.2847
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2687
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2557
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2450
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2358
The value of delta_label of current 6 th iteration is 0.06605682118040285 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3044
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2918
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2813
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2723
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2643
The value of delta_label of current 7 th iteration is 0.052071422288679746 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3156
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3055
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2966
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2888
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2817
The value of delta_label of current 8 th iteration is 0.048992875362828744 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3218
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3131
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3054
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2984
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2920
The value of delta_label of current 9 th iteration is 0.046178203887764974 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3248
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3172
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3104
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3040
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2982
The value of delta_label of current 10 th iteration is 0.035007476471105636 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3256
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3188
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3127
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3069
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3015
The value of delta_label of current 11 th iteration is 0.030345676840531268 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3250
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3189
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3134
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3081
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3032
The value of delta_label of current 12 th iteration is 0.024804292373999472 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3235
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3180
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3131
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3084
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3039
The value of delta_label of current 13 th iteration is 0.02533204327557393 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3214
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3165
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3120
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3078
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3037
The value of delta_label of current 14 th iteration is 0.022165537866127186 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3191
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3146
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3105
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3067
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3029
The value of delta_label of current 15 th iteration is 0.020494326677808074 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3166
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3126
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3088
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3053
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3019
The value of delta_label of current 16 th iteration is 0.01600844401442519 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3143
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3106
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3071
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3039
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3008
The value of delta_label of current 17 th iteration is 0.013017855572169936 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3121
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3087
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3055
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3026
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2996
The value of delta_label of current 18 th iteration is 0.012578063154191221 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3101
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3070
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3040
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3013
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2986
The value of delta_label of current 19 th iteration is 0.011786436801829536 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3081
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3053
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3026
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3001
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2975
The value of delta_label of current 20 th iteration is 0.010467059547893395 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3062
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3036
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3011
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2988
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2963
The value of delta_label of current 21 th iteration is 0.011786436801829536 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3041
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3017
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2994
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2972
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2949
The value of delta_label of current 22 th iteration is 0.008268097457999824 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3019
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2997
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2975
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2955
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2934
The value of delta_label of current 23 th iteration is 0.007300554138446653 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2996
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2976
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2955
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2937
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2917
The value of delta_label of current 24 th iteration is 0.007740346556425367 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2972
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2953
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2934
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2918
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2899
The value of delta_label of current 25 th iteration is 0.0058052599173190255 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2948
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2931
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2913
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2898
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2880
The value of delta_label of current 26 th iteration is 0.004925675081361597 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2924
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2908
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2892
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2878
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2862
The value of delta_label of current 27 th iteration is 0.0047497581141701115 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2901
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2886
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2871
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2858
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2844
The value of delta_label of current 28 th iteration is 0.00562934295012754 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2878
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2865
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2851
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2839
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2826
The value of delta_label of current 29 th iteration is 0.003254463893042484 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2857
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2844
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2831
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2820
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2808
The value of delta_label of current 30 th iteration is 0.0037822147946169407 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2836
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2824
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2812
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2802
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2791
The value of delta_label of current 31 th iteration is 0.003342422376638227 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2816
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2805
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2794
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2785
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2775
The value of delta_label of current 32 th iteration is 0.002726712991468027 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2798
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2788
Epoch 3/5
45/45 [==============================] - 0s 4ms/step - loss: 0.2778
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2769
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2759
The value of delta_label of current 33 th iteration is 0.0025507960242765414 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2781
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2772
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2762
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2754
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2745
The value of delta_label of current 34 th iteration is 0.0024628375406807986 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2766
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2757
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2747
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2739
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2731
The value of delta_label of current 35 th iteration is 0.001847128155510599 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2751
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2743
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2734
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2726
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2718
The value of delta_label of current 36 th iteration is 0.002023045122702085 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2738
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2729
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2721
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2714
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2707
The value of delta_label of current 37 th iteration is 0.001759169671914856 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2725
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2717
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2710
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2703
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2696
The value of delta_label of current 38 th iteration is 0.0029905884422552556 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2713
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2705
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2698
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2692
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2685
The value of delta_label of current 39 th iteration is 0.0021110036062978272 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2701
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2694
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2687
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2681
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2675
The value of delta_label of current 40 th iteration is 0.0023748790570850557 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2690
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2683
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2676
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2670
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2664
The value of delta_label of current 41 th iteration is 0.002726712991468027 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2679
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2672
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2666
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2660
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2654
The value of delta_label of current 42 th iteration is 0.001759169671914856 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2668
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2661
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2655
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2650
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2644
The value of delta_label of current 43 th iteration is 0.003254463893042484 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2657
Epoch 2/5
45/45 [==============================] - 0s 4ms/step - loss: 0.2651
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2645
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2640
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2635
The value of delta_label of current 44 th iteration is 0.003518339343829712 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2646
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2640
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2635
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2630
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2625
The value of delta_label of current 45 th iteration is 0.003254463893042484 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2635
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2630
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2625
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2620
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2615
The value of delta_label of current 46 th iteration is 0.0031665054094467413 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2625
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2620
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2615
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2610
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2606
The value of delta_label of current 47 th iteration is 0.003518339343829712 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2614
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2610
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2605
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2601
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2596
The value of delta_label of current 48 th iteration is 0.0034303808602339694 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2604
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2600
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2595
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2591
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2587
The value of delta_label of current 49 th iteration is 0.0058052599173190255 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2594
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2590
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2586
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2582
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2578
The value of delta_label of current 50 th iteration is 0.007124637171255168 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2584
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2580
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2576
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2573
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2569
The value of delta_label of current 51 th iteration is 0.010115225613510423 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2575
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2571
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2567
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2564
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2560
The value of delta_label of current 52 th iteration is 0.014337232826106078 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2566
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2562
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2558
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2555
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2551
The value of delta_label of current 53 th iteration is 0.019262907907467677 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2556
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2553
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2549
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2546
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2543
The value of delta_label of current 54 th iteration is 0.02911425807019087 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2547
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2544
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2541
Epoch 4/5
45/45 [==============================] - 0s 4ms/step - loss: 0.2538
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2534
The value of delta_label of current 55 th iteration is 0.031137303192892953 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2538
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2535
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2532
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2529
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2526
The value of delta_label of current 56 th iteration is 0.03043363532412701 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2530
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2527
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2524
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2521
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2518
The value of delta_label of current 57 th iteration is 0.02972996745536107 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2522
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2519
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2516
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2513
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2510
The value of delta_label of current 58 th iteration is 0.029554050488169583 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2514
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2511
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2508
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2506
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2503
The value of delta_label of current 59 th iteration is 0.022077579382531444 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2506
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2504
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2501
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2498
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2496
The value of delta_label of current 60 th iteration is 0.021461869997361247 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2499
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2496
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2494
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2491
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2489
The value of delta_label of current 61 th iteration is 0.021637786964552732 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2491
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2489
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2487
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2484
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2482
The value of delta_label of current 62 th iteration is 0.025507960242765415 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2484
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2482
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2480
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2477
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2475
The value of delta_label of current 63 th iteration is 0.029817925938956814 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2477
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2475
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2473
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2471
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2469
The value of delta_label of current 64 th iteration is 0.025947752660744127 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2471
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2469
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2466
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2464
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2462
The value of delta_label of current 65 th iteration is 0.024188582988829272 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2464
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2463
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2461
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2458
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2456
The value of delta_label of current 66 th iteration is 0.025420001759169673 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2458
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2456
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2454
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2452
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2450
The value of delta_label of current 67 th iteration is 0.02665142052951007 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2452
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2450
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2448
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2446
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2444
The value of delta_label of current 68 th iteration is 0.01759169671914856 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2445
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2443
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2442
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2440
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2438
The value of delta_label of current 69 th iteration is 0.003958131761808426 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2440
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2438
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2436
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2434
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2432
The value of delta_label of current 70 th iteration is 0.0030785469258509984 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2434
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2432
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2430
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2428
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2426
The value of delta_label of current 71 th iteration is 0.0030785469258509984 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2428
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2426
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2425
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2423
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2421
The value of delta_label of current 72 th iteration is 0.0037822147946169407 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2422
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2421
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2419
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2417
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2416
The value of delta_label of current 73 th iteration is 0.0029905884422552556 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2417
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2416
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2414
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2412
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2410
The value of delta_label of current 74 th iteration is 0.0026387545078722843 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2412
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2410
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2409
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2407
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2405
The value of delta_label of current 75 th iteration is 0.0037822147946169407 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2407
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2405
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2404
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2402
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2400
The value of delta_label of current 76 th iteration is 0.002286920573489313 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2402
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2400
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2399
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2397
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2395
delta_label  0.0 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
The final prediction cluster is:
0     1775
1     1285
2     1815
3     1102
4      621
5      303
6      306
7      445
8       21
9      501
10     379
11     783
12     303
13     332
14     277
15     512
16     366
17      19
18      83
19     118
20       8
21      15
dtype: int64
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_12"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 24)                768       
=================================================================
Total params: 277,920
Trainable params: 277,920
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=2.0)is: 74.8167040348053
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:31)
computing neighbors
tsne finished and added X_tsne2.0  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap2.0  into the umap coordinates (adata.obsm)

The run time for all resolution is: 107.1918740272522
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6', 'desc_1.8', 'desc_2.0'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6', 'prob_matrix1.8', 'prob_matrix2.0'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6', 'X_Embeded_z1.8', 'X_tsne1.8', 'X_umap1.8', 'X_Embeded_z2.0', 'X_tsne2.0', 'X_umap2.0'
    obsp: 'distances', 'connectivities'
In [30]:
total_clusters
Out[30]:
[6, 9, 9, 10, 11, 13, 13, 15, 17, 19, 22]
In [154]:
#go back and pick a resolution in the middle (0.8) to highlight 
adata = desc.train(adata, dims=[adata.shape[1], 128, 32], tol=0.001, n_neighbors=10,
                   batch_size=256, louvain_resolution=0.8, do_tsne=True, learning_rate=300,
                   do_umap=True, num_Cores_tsne=4)
Start to process resolution= 0.8
The number of cpu in your computer is 12
Create the directory:result_tmp to save result
Checking whether result_tmp/ae_weights.h5  exists in the directory
The file ae_weights.h5 is not exits
Pretraining the 1th layer...
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 1s 7ms/step - loss: 0.5051
Epoch 2/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4777
Epoch 3/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4559
Epoch 4/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4424
Epoch 5/50
45/45 [==============================] - 0s 9ms/step - loss: 0.4326
Epoch 6/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4241
Epoch 7/50
45/45 [==============================] - 0s 6ms/step - loss: 0.4169
Epoch 8/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4113
Epoch 9/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4064
Epoch 10/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4030
Epoch 11/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4000
Epoch 12/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3976
Epoch 13/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3955
Epoch 14/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3938
Epoch 15/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3924
Epoch 16/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3911
Epoch 17/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3900
Epoch 18/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3891
Epoch 19/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3882
Epoch 20/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3873
Epoch 21/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3866
Epoch 22/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3859
Epoch 23/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3852
Epoch 24/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3846
Epoch 25/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3842
Epoch 26/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3835
Epoch 27/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3830
Epoch 28/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3825
Epoch 29/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3819
Epoch 30/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3815
Epoch 31/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3810
Epoch 32/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3806
Epoch 33/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3800
Epoch 34/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3797
Epoch 35/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3792
Epoch 36/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3788
Epoch 37/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3784
Epoch 38/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3782
Epoch 39/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3777
Epoch 40/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3773
Epoch 41/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3770
Epoch 42/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3767
Epoch 43/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3763
Epoch 44/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3761
Epoch 45/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3758
Epoch 46/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3754
Epoch 47/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3751
Epoch 48/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3749
Epoch 49/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3746
Epoch 50/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3744
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3741
Epoch 2/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3742
Epoch 3/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3741
Epoch 4/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3740
Epoch 5/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3740
Epoch 6/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3740
Epoch 7/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3739
Epoch 8/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3741
Epoch 9/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3738
Epoch 10/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3739
Epoch 11/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3739
Epoch 12/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3738
Epoch 13/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3737
Epoch 14/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3738
Epoch 15/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3738
Epoch 16/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3738
Epoch 17/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3737
Epoch 18/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3737
Epoch 19/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3736
Epoch 20/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3736
Epoch 21/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3736
Epoch 22/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3736
Epoch 23/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3736
Epoch 24/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3735
Epoch 25/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3736
Epoch 26/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3735
Epoch 27/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3735
Epoch 28/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3735
Epoch 29/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3733
Epoch 30/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3734
Epoch 31/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3734
Epoch 32/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3734
Epoch 33/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3732
Epoch 34/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3733
Epoch 35/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3733
Epoch 36/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3733
Epoch 37/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3732
Epoch 38/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3733
Epoch 39/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3732
Epoch 40/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 41/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 42/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 43/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 44/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3731
Epoch 45/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 46/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 47/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 48/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 49/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3729
Epoch 50/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 1s 7ms/step - loss: 0.3730
Epoch 2/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 3/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 4/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 5/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 6/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 7/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 8/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3731
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 11/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3730
Epoch 12/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 13/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3728
Epoch 14/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 15/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 16/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 17/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3729
Epoch 00017: early stopping
The 1th layer has been pretrained.
Pretraining the 2th layer...
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 0s 1ms/step - loss: 0.3967
Epoch 2/50
45/45 [==============================] - 0s 900us/step - loss: 0.2189
Epoch 3/50
45/45 [==============================] - 0s 895us/step - loss: 0.1801
Epoch 4/50
45/45 [==============================] - 0s 878us/step - loss: 0.1613
Epoch 5/50
45/45 [==============================] - 0s 896us/step - loss: 0.1512
Epoch 6/50
45/45 [==============================] - 0s 955us/step - loss: 0.1448
Epoch 7/50
45/45 [==============================] - 0s 931us/step - loss: 0.1399
Epoch 8/50
45/45 [==============================] - 0s 911us/step - loss: 0.1374
Epoch 9/50
45/45 [==============================] - 0s 882us/step - loss: 0.1342
Epoch 10/50
45/45 [==============================] - 0s 889us/step - loss: 0.1318
Epoch 11/50
45/45 [==============================] - 0s 874us/step - loss: 0.1307
Epoch 12/50
45/45 [==============================] - 0s 888us/step - loss: 0.1071
Epoch 13/50
45/45 [==============================] - 0s 911us/step - loss: 0.0879
Epoch 14/50
45/45 [==============================] - 0s 943us/step - loss: 0.0861
Epoch 15/50
45/45 [==============================] - 0s 942us/step - loss: 0.0849
Epoch 16/50
45/45 [==============================] - 0s 919us/step - loss: 0.0844
Epoch 17/50
45/45 [==============================] - 0s 884us/step - loss: 0.0836
Epoch 18/50
45/45 [==============================] - 0s 895us/step - loss: 0.0824
Epoch 19/50
45/45 [==============================] - 0s 884us/step - loss: 0.0809
Epoch 20/50
45/45 [==============================] - 0s 884us/step - loss: 0.0818
Epoch 21/50
45/45 [==============================] - 0s 905us/step - loss: 0.0807
Epoch 22/50
45/45 [==============================] - 0s 910us/step - loss: 0.0799
Epoch 23/50
45/45 [==============================] - 0s 873us/step - loss: 0.0798
Epoch 24/50
45/45 [==============================] - 0s 900us/step - loss: 0.0788
Epoch 25/50
45/45 [==============================] - 0s 871us/step - loss: 0.0782
Epoch 26/50
45/45 [==============================] - 0s 895us/step - loss: 0.0772
Epoch 27/50
45/45 [==============================] - 0s 898us/step - loss: 0.0771
Epoch 28/50
45/45 [==============================] - 0s 891us/step - loss: 0.0769
Epoch 29/50
45/45 [==============================] - 0s 894us/step - loss: 0.0762
Epoch 30/50
45/45 [==============================] - 0s 901us/step - loss: 0.0753
Epoch 31/50
45/45 [==============================] - 0s 961us/step - loss: 0.0759
Epoch 32/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0751
Epoch 33/50
45/45 [==============================] - 0s 999us/step - loss: 0.0752
Epoch 34/50
45/45 [==============================] - 0s 941us/step - loss: 0.0753
Epoch 35/50
45/45 [==============================] - 0s 964us/step - loss: 0.0745
Epoch 36/50
45/45 [==============================] - 0s 939us/step - loss: 0.0739
Epoch 37/50
45/45 [==============================] - 0s 930us/step - loss: 0.0739
Epoch 38/50
45/45 [==============================] - 0s 936us/step - loss: 0.0738
Epoch 39/50
45/45 [==============================] - 0s 940us/step - loss: 0.0732
Epoch 40/50
45/45 [==============================] - 0s 935us/step - loss: 0.0726
Epoch 41/50
45/45 [==============================] - 0s 944us/step - loss: 0.0730
Epoch 42/50
45/45 [==============================] - 0s 936us/step - loss: 0.0732
Epoch 43/50
45/45 [==============================] - 0s 952us/step - loss: 0.0727
Epoch 44/50
45/45 [==============================] - 0s 938us/step - loss: 0.0719
Epoch 45/50
45/45 [==============================] - 0s 926us/step - loss: 0.0723
Epoch 46/50
45/45 [==============================] - 0s 952us/step - loss: 0.0713
Epoch 47/50
45/45 [==============================] - 0s 931us/step - loss: 0.0712
Epoch 48/50
45/45 [==============================] - 0s 934us/step - loss: 0.0707
Epoch 49/50
45/45 [==============================] - 0s 928us/step - loss: 0.0715
Epoch 50/50
45/45 [==============================] - 0s 905us/step - loss: 0.0715
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 0s 968us/step - loss: 0.0711
Epoch 2/50
45/45 [==============================] - 0s 941us/step - loss: 0.0706
Epoch 3/50
45/45 [==============================] - 0s 918us/step - loss: 0.0707
Epoch 4/50
45/45 [==============================] - 0s 904us/step - loss: 0.0711
Epoch 5/50
45/45 [==============================] - 0s 908us/step - loss: 0.0710
Epoch 6/50
45/45 [==============================] - 0s 871us/step - loss: 0.0710
Epoch 7/50
45/45 [==============================] - 0s 914us/step - loss: 0.0709
Epoch 8/50
45/45 [==============================] - 0s 878us/step - loss: 0.0709
Epoch 9/50
45/45 [==============================] - 0s 939us/step - loss: 0.0705
Epoch 10/50
45/45 [==============================] - 0s 875us/step - loss: 0.0699
Epoch 11/50
45/45 [==============================] - 0s 926us/step - loss: 0.0709
Epoch 12/50
45/45 [==============================] - 0s 933us/step - loss: 0.0697
Epoch 13/50
45/45 [==============================] - 0s 912us/step - loss: 0.0699
Epoch 14/50
45/45 [==============================] - 0s 920us/step - loss: 0.0701
Epoch 15/50
45/45 [==============================] - 0s 900us/step - loss: 0.0700
Epoch 16/50
45/45 [==============================] - 0s 932us/step - loss: 0.0705
Epoch 17/50
45/45 [==============================] - 0s 886us/step - loss: 0.0704
Epoch 18/50
45/45 [==============================] - 0s 917us/step - loss: 0.0703
Epoch 19/50
45/45 [==============================] - 0s 890us/step - loss: 0.0695
Epoch 20/50
45/45 [==============================] - 0s 958us/step - loss: 0.0706
Epoch 21/50
45/45 [==============================] - 0s 930us/step - loss: 0.0703
Epoch 22/50
45/45 [==============================] - 0s 924us/step - loss: 0.0701
Epoch 23/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0708
Epoch 24/50
45/45 [==============================] - 0s 881us/step - loss: 0.0703
Epoch 25/50
45/45 [==============================] - 0s 876us/step - loss: 0.0704
Epoch 26/50
45/45 [==============================] - 0s 901us/step - loss: 0.0700
Epoch 27/50
45/45 [==============================] - 0s 912us/step - loss: 0.0705
Epoch 28/50
45/45 [==============================] - 0s 903us/step - loss: 0.0705
Epoch 29/50
45/45 [==============================] - 0s 887us/step - loss: 0.0703
Epoch 00029: early stopping
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 0s 976us/step - loss: 0.0704
Epoch 2/50
45/45 [==============================] - 0s 953us/step - loss: 0.0701
Epoch 3/50
45/45 [==============================] - 0s 947us/step - loss: 0.0702
Epoch 4/50
45/45 [==============================] - 0s 932us/step - loss: 0.0706
Epoch 5/50
45/45 [==============================] - 0s 922us/step - loss: 0.0706
Epoch 6/50
45/45 [==============================] - 0s 911us/step - loss: 0.0705
Epoch 7/50
45/45 [==============================] - 0s 906us/step - loss: 0.0706
Epoch 8/50
45/45 [==============================] - 0s 911us/step - loss: 0.0706
Epoch 9/50
45/45 [==============================] - 0s 904us/step - loss: 0.0701
Epoch 10/50
45/45 [==============================] - 0s 889us/step - loss: 0.0696
Epoch 11/50
45/45 [==============================] - 0s 940us/step - loss: 0.0706
Epoch 12/50
45/45 [==============================] - 0s 929us/step - loss: 0.0693
Epoch 13/50
45/45 [==============================] - 0s 875us/step - loss: 0.0697
Epoch 14/50
45/45 [==============================] - 0s 889us/step - loss: 0.0698
Epoch 15/50
45/45 [==============================] - 0s 905us/step - loss: 0.0697
Epoch 16/50
45/45 [==============================] - 0s 902us/step - loss: 0.0703
Epoch 17/50
45/45 [==============================] - 0s 910us/step - loss: 0.0701
Epoch 18/50
45/45 [==============================] - 0s 890us/step - loss: 0.0701
Epoch 19/50
45/45 [==============================] - 0s 917us/step - loss: 0.0693
Epoch 20/50
45/45 [==============================] - 0s 899us/step - loss: 0.0704
Epoch 21/50
45/45 [==============================] - 0s 911us/step - loss: 0.0701
Epoch 22/50
45/45 [==============================] - 0s 909us/step - loss: 0.0700
Epoch 00022: early stopping
The 2th layer has been pretrained.
Copying layer-wise pretrained weights to deep autoencoders
Fine-tuning autoencoder end-to-end
learning rate = 1
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3707
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3694
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3686
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3680
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3674
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3669
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3664
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3660
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3656
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3652
Epoch 11/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3648
Epoch 12/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3644
Epoch 13/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3640
Epoch 14/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3637
Epoch 15/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3634
Epoch 16/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3630
Epoch 17/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3627
Epoch 18/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3624
Epoch 19/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3621
Epoch 20/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3619
Epoch 21/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3616
Epoch 22/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3613
Epoch 23/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3611
Epoch 24/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3608
Epoch 25/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3606
Epoch 26/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3603
Epoch 27/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3601
Epoch 28/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3599
Epoch 29/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3596
Epoch 30/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3594
Epoch 31/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3592
Epoch 32/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3590
Epoch 33/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3588
Epoch 34/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3586
Epoch 35/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3584
Epoch 36/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3582
Epoch 37/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3580
Epoch 38/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 39/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3577
Epoch 40/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3575
Epoch 41/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3573
Epoch 42/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3572
Epoch 43/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3570
Epoch 44/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3568
Epoch 45/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3567
Epoch 46/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3565
Epoch 47/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3564
Epoch 48/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3562
Epoch 49/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3561
Epoch 50/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3559
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3555
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3554
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3554
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3554
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3553
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3553
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3553
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3553
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3553
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3553
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3553
Epoch 12/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3552
Epoch 13/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3552
Epoch 14/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3552
Epoch 15/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3552
Epoch 16/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3552
Epoch 17/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3552
Epoch 18/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3552
Epoch 19/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3551
Epoch 20/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3551
Epoch 21/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3551
Epoch 22/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3551
Epoch 23/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3551
Epoch 24/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3551
Epoch 25/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3551
Epoch 26/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3550
Epoch 27/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3550
Epoch 28/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3550
Epoch 29/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3550
Epoch 30/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3550
Epoch 31/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3550
Epoch 32/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3550
Epoch 33/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 34/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 35/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 36/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 37/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 38/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 39/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3549
Epoch 40/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3548
Epoch 41/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 42/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 43/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 44/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 45/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 46/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 47/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3548
Epoch 48/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 49/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3547
Epoch 50/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3547
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 1s 6ms/step - loss: 0.3547
Epoch 2/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3547
Epoch 3/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3547
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 6/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3547
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3547
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 11/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 00011: early stopping
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 2/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 3/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 5/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 6/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 7/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 00011: early stopping
learning rate = 0.0001
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 00011: early stopping
learning rate = 1e-05
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 5/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 8/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3546
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3546
Epoch 00011: early stopping
Pretraining time is 77.77368402481079
Pretrained weights are saved to result_tmp /ae_weights.h5
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 11 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.052159380772275485 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0894
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0730
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0641
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0568
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0507
The value of delta_label of current 2 th iteration is 0.021110036062978274 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1482
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1251
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1071
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0931
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0821
The value of delta_label of current 3 th iteration is 0.010906851965872108 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1813
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1565
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1367
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1210
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1086
The value of delta_label of current 4 th iteration is 0.011082768933063593 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2061
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1810
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1621
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1479
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1368
The value of delta_label of current 5 th iteration is 0.008883806843170024 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2221
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2034
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1891
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1779
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1687
The value of delta_label of current 6 th iteration is 0.008531972908787053 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2239
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2119
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2020
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1936
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1864
The value of delta_label of current 7 th iteration is 0.0063330108188934826 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2186
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2101
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2027
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1961
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1902
The value of delta_label of current 8 th iteration is 0.005189550532148826 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2114
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2048
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1990
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1937
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1889
The value of delta_label of current 9 th iteration is 0.0031665054094467413 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2041
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1988
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1940
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1897
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1857
The value of delta_label of current 10 th iteration is 0.0024628375406807986 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1972
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1928
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1888
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1852
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1818
The value of delta_label of current 11 th iteration is 0.0015832527047233706 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1907
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1871
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1837
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1807
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1778
The value of delta_label of current 12 th iteration is 0.0013193772539361421 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1848
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1817
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1790
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1764
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1739
The value of delta_label of current 13 th iteration is 0.0010555018031489136 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1794
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1768
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1745
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1723
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1702
delta_label  0.0006157093851701996 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is:
0     2487
1     2235
2     2137
3     1576
4     1252
5      446
6      393
7      331
8      318
9      138
10      56
dtype: int64
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_12"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 11)                352       
=================================================================
Total params: 277,504
Trainable params: 277,504
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.8)is: 91.67204809188843
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne0.8  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.8  into the umap coordinates (adata.obsm)

The run time for all resolution is: 123.88686084747314
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.8'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.8'
    obsm: 'X_Embeded_z0.8', 'X_tsne', 'X_tsne0.8', 'X_umap', 'X_umap0.8'
    obsp: 'distances', 'connectivities'
In [155]:
adata
Out[155]:
AnnData object with n_obs × n_vars = 11369 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.8'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.8'
    obsm: 'X_Embeded_z0.8', 'X_tsne', 'X_tsne0.8', 'X_umap', 'X_umap0.8'
    obsp: 'distances', 'connectivities'
In [156]:
prob_1=adata.uns["prob_matrix0.8"]
adata.obs["max.prob0.8"]=np.max(prob_1,axis=1)
#tSNE plot 
sc.pl.scatter(adata,basis="tsne0.8",color=['desc_0.8'])
sc.pl.scatter(adata,basis="tsne0.8",color=["max.prob0.8"], legend_fontoutline=5)
In [157]:
from matplotlib.pyplot import rc_context
with rc_context({'figure.figsize': (5, 5)}):
    sc.pl.tsne(adata,color=['desc_0.8',"max.prob0.8"], legend_loc='on data',
                  legend_fontsize=10, legend_fontoutline=2,frameon=False, title='10x-V3', 
               add_outline=True, outline_width=(0.5, 0.05), vmin=0.1,vmax=0.8, ncols=1, 
               save='DESC_Control_Res0.8_TSNE_Prrobabilities.png')
    
WARNING: The title list is shorter than the number of panels. Using 'color' value instead for some plots.
WARNING: saving figure to file figures/tsneDESC_Control_Res0.8_TSNE_Prrobabilities.png

scCLEAN¶

Repeat the exact same framework except switching out the input file from Control to scCLEAN

In [158]:
#input the cellranger output h5ad file from alignment to the full transcriptome
data = desc.read_h5ad('raw_files/FUll_transcriptome/Dep_rep3_not_masked_filtered_feature_bc_matrix.h5ad')
data.var_names_make_unique()
data
Variable names are not unique. To make them unique, call `.var_names_make_unique`.
Out[158]:
AnnData object with n_obs × n_vars = 11786 × 36601
    var: 'gene_ids', 'feature_types', 'genome'
In [159]:
sc.pp.filter_cells(data, min_counts=500)
sc.pp.filter_cells(data, min_genes=200)
sc.pp.filter_genes(data, min_cells=3)
filtered out 248 cells that have less than 200 genes expressed
filtered out 15160 genes that are detected in less than 3 cells
In [160]:
mito_genes = data.var_names.str.startswith('MT-')
# for each cell compute fraction of counts in mito genes vs. all genes
# the `.A1` is only necessary as X is sparse (to transform to a dense array after summing)
data.obs['percent_mito'] = np.sum(
    data[:, mito_genes].X, axis=1).A1 / np.sum(data.X, axis=1).A1
# add the total counts per cell as observations-annotation to adata
data.obs['n_counts'] = data.X.sum(axis=1).A1
In [161]:
#determine the proper thresholds according to the 99% of the data
per_cell_metrics = data.obs
dquantile = pd.DataFrame()
dquantile = per_cell_metrics.quantile(0.99, numeric_only=True)
dquantile
Out[161]:
n_counts        13217.910000
n_genes          4809.150000
percent_mito        0.001973
Name: 0.99, dtype: float64

Remember the overall counts are lower in the scCLEAN condition because 250 protein coding genes were targeted for removal, and reads were re-distributed to lower expressed transcripts. Consequently, the UMIs associated with housekeeping genes were removed.

In [162]:
sc.pl.violin(data, ['n_genes', 'n_counts', 'percent_mito'],jitter=0.4, multi_panel=True)
In [163]:
#filter thresholds from 99% 
data = data[data.obs['n_counts'] < 13217.910000, :]
data
Out[163]:
View of AnnData object with n_obs × n_vars = 11422 × 21441
    obs: 'n_counts', 'n_genes', 'percent_mito'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells'
In [164]:
desc.normalize_per_cell(data, counts_per_cell_after=1e4)
normalizing by total count per cell
Trying to set attribute `.obs` of view, copying.
    finished (0:00:00): normalized adata.X and added    'n_counts', counts per cell before normalization (adata.obs)
In [165]:
desc.log1p(data)
In [166]:
data.raw=data
In [167]:
sc.pp.highly_variable_genes(data, min_mean=0.0125, max_mean=3, min_disp=0.5, subset=True)
extracting highly variable genes
    finished (0:00:00)
--> added
    'highly_variable', boolean vector (adata.var)
    'means', float vector (adata.var)
    'dispersions', float vector (adata.var)
    'dispersions_norm', float vector (adata.var)
In [168]:
data = data[:, data.var['highly_variable']]
data
Out[168]:
View of AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm'
    uns: 'log1p', 'hvg'
In [169]:
desc.scale(data, zero_center=True, max_value=3)
/Users/jbezney/opt/anaconda3/envs/DESC/lib/python3.6/site-packages/scanpy/preprocessing/_simple.py:845: UserWarning: Revieved a view of an AnnData. Making a copy.
  view_to_actual(adata)
... as `zero_center=True`, sparse input is densified and may lead to large memory consumption
In [44]:
#loop through the deep learning model and append the total number of clusters identified
#check the total number of clusters according to the resolution with which it was identified
resolution_x = [0.1,0.2,0.4,0.6,0.8,1.0,1.2,1.4,1.6,1.8,2.0]
dep_total_clusters = []
for value in resolution_x:
    data = desc.train(data, dims=[data.shape[1], 128, 32], tol=0.001, n_neighbors=10,
                   batch_size=256, louvain_resolution=[value], do_tsne=True, learning_rate=300,
                   do_umap=True, num_Cores_tsne=4)
    df_cluster = pd.DataFrame(data.obs['desc_'+str(value)])
    df_cluster = len(df_cluster.iloc[:,0].unique())
    dep_total_clusters.append(df_cluster)
Start to process resolution= 0.1
The number of cpu in your computer is 12
Create the directory:result_tmp to save result
Checking whether result_tmp/ae_weights.h5  exists in the directory
The file ae_weights.h5 is not exits
Pretraining the 1th layer...
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 1s 7ms/step - loss: 0.4919
Epoch 2/50
45/45 [==============================] - 0s 8ms/step - loss: 0.4660
Epoch 3/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4452
Epoch 4/50
45/45 [==============================] - 0s 8ms/step - loss: 0.4307
Epoch 5/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4200
Epoch 6/50
45/45 [==============================] - 0s 8ms/step - loss: 0.4102
Epoch 7/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4020
Epoch 8/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3955
Epoch 9/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3908
Epoch 10/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3872
Epoch 11/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3844
Epoch 12/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3824
Epoch 13/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3805
Epoch 14/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3791
Epoch 15/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3778
Epoch 16/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3767
Epoch 17/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3757
Epoch 18/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3747
Epoch 19/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3740
Epoch 20/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3731
Epoch 21/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3725
Epoch 22/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3717
Epoch 23/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3710
Epoch 24/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3704
Epoch 25/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3697
Epoch 26/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3689
Epoch 27/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3684
Epoch 28/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3678
Epoch 29/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3673
Epoch 30/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3667
Epoch 31/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3663
Epoch 32/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3656
Epoch 33/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3653
Epoch 34/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3648
Epoch 35/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3643
Epoch 36/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3637
Epoch 37/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3634
Epoch 38/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3629
Epoch 39/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3625
Epoch 40/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3621
Epoch 41/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3618
Epoch 42/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3614
Epoch 43/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3611
Epoch 44/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3608
Epoch 45/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3604
Epoch 46/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3600
Epoch 47/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3598
Epoch 48/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3594
Epoch 49/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3592
Epoch 50/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3589
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 2/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3586
Epoch 3/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 4/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 5/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3586
Epoch 6/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 7/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3586
Epoch 8/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3585
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3584
Epoch 11/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3584
Epoch 12/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3583
Epoch 13/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3583
Epoch 14/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3583
Epoch 15/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3582
Epoch 16/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3582
Epoch 17/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3582
Epoch 18/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3582
Epoch 19/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3582
Epoch 20/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3581
Epoch 21/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3582
Epoch 22/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3582
Epoch 23/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3581
Epoch 24/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3581
Epoch 25/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3581
Epoch 26/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3579
Epoch 27/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3580
Epoch 28/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 29/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 30/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 31/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3579
Epoch 32/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3578
Epoch 33/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 34/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 35/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3578
Epoch 36/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3577
Epoch 37/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3578
Epoch 38/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3577
Epoch 39/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 40/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 41/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3577
Epoch 42/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 43/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 44/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3576
Epoch 45/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 46/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3575
Epoch 47/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3575
Epoch 48/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3574
Epoch 49/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
Epoch 50/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3573
Epoch 2/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
Epoch 3/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3573
Epoch 4/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3573
Epoch 5/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
Epoch 6/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3574
Epoch 7/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3575
Epoch 8/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3574
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
Epoch 11/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3574
Epoch 00011: early stopping
The 1th layer has been pretrained.
Pretraining the 2th layer...
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 0s 1ms/step - loss: 0.3968
Epoch 2/50
45/45 [==============================] - 0s 932us/step - loss: 0.1693
Epoch 3/50
45/45 [==============================] - 0s 970us/step - loss: 0.1313
Epoch 4/50
45/45 [==============================] - 0s 949us/step - loss: 0.1164
Epoch 5/50
45/45 [==============================] - 0s 937us/step - loss: 0.1076
Epoch 6/50
45/45 [==============================] - 0s 972us/step - loss: 0.1024
Epoch 7/50
45/45 [==============================] - 0s 954us/step - loss: 0.0984
Epoch 8/50
45/45 [==============================] - 0s 929us/step - loss: 0.0955
Epoch 9/50
45/45 [==============================] - 0s 967us/step - loss: 0.0932
Epoch 10/50
45/45 [==============================] - 0s 971us/step - loss: 0.0909
Epoch 11/50
45/45 [==============================] - 0s 933us/step - loss: 0.0885
Epoch 12/50
45/45 [==============================] - 0s 944us/step - loss: 0.0866
Epoch 13/50
45/45 [==============================] - 0s 927us/step - loss: 0.0851
Epoch 14/50
45/45 [==============================] - 0s 981us/step - loss: 0.0841
Epoch 15/50
45/45 [==============================] - 0s 955us/step - loss: 0.0831
Epoch 16/50
45/45 [==============================] - 0s 928us/step - loss: 0.0820
Epoch 17/50
45/45 [==============================] - 0s 959us/step - loss: 0.0814
Epoch 18/50
45/45 [==============================] - 0s 989us/step - loss: 0.0799
Epoch 19/50
45/45 [==============================] - 0s 953us/step - loss: 0.0800
Epoch 20/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0787
Epoch 21/50
45/45 [==============================] - 0s 975us/step - loss: 0.0781
Epoch 22/50
45/45 [==============================] - 0s 950us/step - loss: 0.0775
Epoch 23/50
45/45 [==============================] - 0s 991us/step - loss: 0.0772
Epoch 24/50
45/45 [==============================] - 0s 967us/step - loss: 0.0766
Epoch 25/50
45/45 [==============================] - 0s 957us/step - loss: 0.0757
Epoch 26/50
45/45 [==============================] - 0s 924us/step - loss: 0.0759
Epoch 27/50
45/45 [==============================] - 0s 986us/step - loss: 0.0750
Epoch 28/50
45/45 [==============================] - 0s 932us/step - loss: 0.0744
Epoch 29/50
45/45 [==============================] - 0s 958us/step - loss: 0.0746
Epoch 30/50
45/45 [==============================] - 0s 948us/step - loss: 0.0733
Epoch 31/50
45/45 [==============================] - 0s 965us/step - loss: 0.0729
Epoch 32/50
45/45 [==============================] - 0s 967us/step - loss: 0.0730
Epoch 33/50
45/45 [==============================] - 0s 966us/step - loss: 0.0727
Epoch 34/50
45/45 [==============================] - 0s 935us/step - loss: 0.0726
Epoch 35/50
45/45 [==============================] - 0s 969us/step - loss: 0.0716
Epoch 36/50
45/45 [==============================] - 0s 957us/step - loss: 0.0716
Epoch 37/50
45/45 [==============================] - 0s 936us/step - loss: 0.0721
Epoch 38/50
45/45 [==============================] - 0s 978us/step - loss: 0.0709
Epoch 39/50
45/45 [==============================] - 0s 991us/step - loss: 0.0715
Epoch 40/50
45/45 [==============================] - 0s 943us/step - loss: 0.0706
Epoch 41/50
45/45 [==============================] - 0s 982us/step - loss: 0.0707
Epoch 42/50
45/45 [==============================] - 0s 952us/step - loss: 0.0705
Epoch 43/50
45/45 [==============================] - 0s 945us/step - loss: 0.0704
Epoch 44/50
45/45 [==============================] - 0s 984us/step - loss: 0.0696
Epoch 45/50
45/45 [==============================] - 0s 958us/step - loss: 0.0701
Epoch 46/50
45/45 [==============================] - 0s 941us/step - loss: 0.0697
Epoch 47/50
45/45 [==============================] - 0s 992us/step - loss: 0.0695
Epoch 48/50
45/45 [==============================] - 0s 957us/step - loss: 0.0697
Epoch 49/50
45/45 [==============================] - 0s 949us/step - loss: 0.0699
Epoch 50/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0691
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 0s 962us/step - loss: 0.0691
Epoch 2/50
45/45 [==============================] - 0s 920us/step - loss: 0.0689
Epoch 3/50
45/45 [==============================] - 0s 922us/step - loss: 0.0694
Epoch 4/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0690
Epoch 5/50
45/45 [==============================] - 0s 942us/step - loss: 0.0691
Epoch 6/50
45/45 [==============================] - 0s 913us/step - loss: 0.0689
Epoch 7/50
45/45 [==============================] - 0s 921us/step - loss: 0.0689
Epoch 8/50
45/45 [==============================] - 0s 932us/step - loss: 0.0688
Epoch 9/50
45/45 [==============================] - 0s 908us/step - loss: 0.0688
Epoch 10/50
45/45 [==============================] - 0s 923us/step - loss: 0.0692
Epoch 11/50
45/45 [==============================] - 0s 936us/step - loss: 0.0691
Epoch 12/50
45/45 [==============================] - 0s 934us/step - loss: 0.0688
Epoch 13/50
45/45 [==============================] - 0s 917us/step - loss: 0.0684
Epoch 14/50
45/45 [==============================] - 0s 923us/step - loss: 0.0689
Epoch 15/50
45/45 [==============================] - 0s 938us/step - loss: 0.0690
Epoch 16/50
45/45 [==============================] - 0s 917us/step - loss: 0.0689
Epoch 17/50
45/45 [==============================] - 0s 937us/step - loss: 0.0690
Epoch 18/50
45/45 [==============================] - 0s 903us/step - loss: 0.0687
Epoch 19/50
45/45 [==============================] - 0s 933us/step - loss: 0.0693
Epoch 20/50
45/45 [==============================] - 0s 894us/step - loss: 0.0687
Epoch 21/50
45/45 [==============================] - 0s 941us/step - loss: 0.0688
Epoch 22/50
45/45 [==============================] - 0s 925us/step - loss: 0.0688
Epoch 23/50
45/45 [==============================] - 0s 926us/step - loss: 0.0690
Epoch 00023: early stopping
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0687
Epoch 2/50
45/45 [==============================] - 0s 943us/step - loss: 0.0686
Epoch 3/50
45/45 [==============================] - 0s 950us/step - loss: 0.0691
Epoch 4/50
45/45 [==============================] - 0s 944us/step - loss: 0.0687
Epoch 5/50
45/45 [==============================] - 0s 980us/step - loss: 0.0688
Epoch 6/50
45/45 [==============================] - 0s 971us/step - loss: 0.0686
Epoch 7/50
45/45 [==============================] - 0s 911us/step - loss: 0.0687
Epoch 8/50
45/45 [==============================] - 0s 927us/step - loss: 0.0686
Epoch 9/50
45/45 [==============================] - 0s 926us/step - loss: 0.0685
Epoch 10/50
45/45 [==============================] - 0s 964us/step - loss: 0.0690
Epoch 11/50
45/45 [==============================] - 0s 944us/step - loss: 0.0688
Epoch 12/50
45/45 [==============================] - 0s 954us/step - loss: 0.0686
Epoch 00012: early stopping
The 2th layer has been pretrained.
Copying layer-wise pretrained weights to deep autoencoders
Fine-tuning autoencoder end-to-end
learning rate = 1
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3541
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3525
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3515
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3508
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3503
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3497
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3492
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3488
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3483
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3479
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3475
Epoch 12/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3471
Epoch 13/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3466
Epoch 14/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3462
Epoch 15/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3459
Epoch 16/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3455
Epoch 17/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3451
Epoch 18/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3448
Epoch 19/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3445
Epoch 20/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3441
Epoch 21/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3438
Epoch 22/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3435
Epoch 23/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3432
Epoch 24/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3430
Epoch 25/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3427
Epoch 26/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3425
Epoch 27/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3422
Epoch 28/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3420
Epoch 29/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3417
Epoch 30/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3415
Epoch 31/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3413
Epoch 32/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3411
Epoch 33/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3408
Epoch 34/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3406
Epoch 35/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3404
Epoch 36/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3402
Epoch 37/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3400
Epoch 38/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3398
Epoch 39/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3396
Epoch 40/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3395
Epoch 41/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3393
Epoch 42/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3391
Epoch 43/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3389
Epoch 44/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3388
Epoch 45/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3386
Epoch 46/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3384
Epoch 47/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3383
Epoch 48/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3381
Epoch 49/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3380
Epoch 50/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3378
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3374
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3373
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3373
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 8/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3372
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 12/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 13/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 14/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 15/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 16/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 17/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 18/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 19/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 20/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 21/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 22/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 23/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 24/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 25/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 26/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 27/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 28/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 29/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 30/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 31/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 32/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 33/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 34/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 35/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 36/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 37/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 38/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 39/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 40/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 41/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 42/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 43/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 44/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 45/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3367
Epoch 46/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3366
Epoch 47/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3366
Epoch 48/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3366
Epoch 49/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3366
Epoch 50/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3366
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 00011: early stopping
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 00011: early stopping
learning rate = 0.0001
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 00011: early stopping
learning rate = 1e-05
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 00011: early stopping
Pretraining time is 75.50488686561584
Pretrained weights are saved to result_tmp /ae_weights.h5
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 8 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.03449483452985467 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0931
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0702
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0575
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0487
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0420
The value of delta_label of current 2 th iteration is 0.016897215899142008 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1406
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1140
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0950
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0807
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0698
The value of delta_label of current 3 th iteration is 0.010506040973559796 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1567
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1315
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1131
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0998
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0902
The value of delta_label of current 4 th iteration is 0.009805638241989144 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1629
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1414
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1267
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1163
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1086
The value of delta_label of current 5 th iteration is 0.010506040973559796 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1622
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1489
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1392
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1317
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1257
The value of delta_label of current 6 th iteration is 0.007529329364384521 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1561
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1486
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1425
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1373
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1328
The value of delta_label of current 7 th iteration is 0.003939765365084924 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1488
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1438
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1395
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1356
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1321
The value of delta_label of current 8 th iteration is 0.002889161267728944 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1422
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1384
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1351
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1320
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1292
The value of delta_label of current 9 th iteration is 0.0019261075118192962 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1362
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1332
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1306
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1281
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1257
The value of delta_label of current 10 th iteration is 0.001751006828926633 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1309
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1285
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1263
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1242
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1223
The value of delta_label of current 11 th iteration is 0.0016634564874803011 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1264
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1244
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1226
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1208
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1192
delta_label  0.0009630537559096481 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0    4260
1    2062
2    1632
3    1789
4     790
5     388
6     318
7     183
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_15"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 8)                 256       
=================================================================
Total params: 277,408
Trainable params: 277,408
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.1)is: 87.4849910736084
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:32)
computing neighbors
tsne finished and added X_tsne0.1  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.1  into the umap coordinates (adata.obsm)

The run time for all resolution is: 121.3835871219635
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1'
    obsp: 'distances', 'connectivities'
Start to process resolution= 0.2
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.016829729080200195
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 9 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.038171948870600596 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0946
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0730
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0605
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0516
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0448
The value of delta_label of current 2 th iteration is 0.01645946419191035 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1416
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1159
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0971
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0830
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0722
The value of delta_label of current 3 th iteration is 0.009017685168972158 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1588
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1340
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1160
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1031
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0937
The value of delta_label of current 4 th iteration is 0.009980738924881808 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1668
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1454
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1308
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1204
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1128
The value of delta_label of current 5 th iteration is 0.009280336193311154 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1683
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1545
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1446
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1369
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1307
The value of delta_label of current 6 th iteration is 0.007879530730169847 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1635
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1555
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1491
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1437
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1391
The value of delta_label of current 7 th iteration is 0.005690772194011557 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1565
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1513
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1469
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1429
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1393
The value of delta_label of current 8 th iteration is 0.002889161267728944 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1500
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1462
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1427
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1396
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1366
The value of delta_label of current 9 th iteration is 0.0025389599019436174 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1442
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1411
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1384
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1358
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1333
The value of delta_label of current 10 th iteration is 0.0014008054631413063 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1390
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1365
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1342
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1321
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1300
The value of delta_label of current 11 th iteration is 0.001225704780248643 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1345
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1325
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1306
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1288
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1271
The value of delta_label of current 12 th iteration is 0.0011381544388023113 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1306
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1289
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1273
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1258
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1243
delta_label  0.0007004027315706532 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
The final prediction cluster is:
0    4271
1    2020
2    1639
3    1785
4     787
5     378
6     300
7     161
8      81
dtype: int64
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_16"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 9)                 288       
=================================================================
Total params: 277,440
Trainable params: 277,440
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.2)is: 13.29884123802185
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne0.2  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.2  into the umap coordinates (adata.obsm)

The run time for all resolution is: 44.709169149398804
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2'
    obsp: 'distances', 'connectivities'
Start to process resolution= 0.4
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.01116180419921875
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 11 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.04377517072316582 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1021
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0802
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0675
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0585
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.0515
The value of delta_label of current 2 th iteration is 0.031343022237786726 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1564
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1300
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1111
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0967
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0855
The value of delta_label of current 3 th iteration is 0.02775345823848713 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1806
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1561
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1382
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1249
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1149
The value of delta_label of current 4 th iteration is 0.023813692873402206 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1964
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1757
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1610
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1501
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1417
The value of delta_label of current 5 th iteration is 0.019523726142531957 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2069
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1921
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1811
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1726
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1655
The value of delta_label of current 6 th iteration is 0.014620907021537384 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2085
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1983
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1899
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1830
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1770
The value of delta_label of current 7 th iteration is 0.010768691997898792 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.2047
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1970
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1904
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1847
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1796
The value of delta_label of current 8 th iteration is 0.0074417790229381895 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1986
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1927
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1873
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1826
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1784
The value of delta_label of current 9 th iteration is 0.005077919803887235 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1920
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1873
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1831
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1793
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1757
The value of delta_label of current 10 th iteration is 0.002889161267728944 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1857
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1820
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1786
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1756
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1727
The value of delta_label of current 11 th iteration is 0.002451409560497286 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1800
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1771
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1744
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1720
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1696
The value of delta_label of current 12 th iteration is 0.001225704780248643 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1751
Epoch 2/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1727
Epoch 3/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1705
Epoch 4/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1685
Epoch 5/5
45/45 [==============================] - 0s 2ms/step - loss: 0.1665
delta_label  0.0006128523901243215 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0     3134
1     2018
2     1628
3     1437
4      782
5      331
6     1488
7      310
8       77
9      145
10      72
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_17"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 11)                352       
=================================================================
Total params: 277,504
Trainable params: 277,504
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.4)is: 12.697240114212036
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.4  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.4  into the umap coordinates (adata.obsm)

The run time for all resolution is: 42.61803412437439
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4'
    obsp: 'distances', 'connectivities'
Start to process resolution= 0.6
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.011688947677612305
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 15 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:00)
The value of delta_label of current 1 th iteration is 0.06478725267028541 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1202
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0987
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0859
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0766
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0692
The value of delta_label of current 2 th iteration is 0.03633339170022763 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1806
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1562
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1380
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1236
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1121
The value of delta_label of current 3 th iteration is 0.031868324286464716 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2137
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1904
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1726
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1587
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1479
The value of delta_label of current 4 th iteration is 0.02827876028716512 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2366
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2174
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2029
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1915
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1824
The value of delta_label of current 5 th iteration is 0.02889161267728944 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2552
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2406
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2292
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2200
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2122
The value of delta_label of current 6 th iteration is 0.022587988093153565 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2670
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2559
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2466
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2386
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2317
The value of delta_label of current 7 th iteration is 0.018035370337944317 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2723
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2632
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2551
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2481
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2418
The value of delta_label of current 8 th iteration is 0.01540886009455437 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2730
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2652
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2582
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2520
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2464
The value of delta_label of current 9 th iteration is 0.007704430047277185 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2710
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2643
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2583
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2530
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2480
The value of delta_label of current 10 th iteration is 0.00586587287690422 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2674
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2617
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2566
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2520
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2477
The value of delta_label of current 11 th iteration is 0.003502013657853266 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2630
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2581
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2538
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2497
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2459
The value of delta_label of current 12 th iteration is 0.003502013657853266 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2582
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2539
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2501
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2465
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2430
The value of delta_label of current 13 th iteration is 0.0023638592190509543 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2531
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2493
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2460
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2426
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2395
The value of delta_label of current 14 th iteration is 0.0014008054631413063 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2479
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2445
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2415
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2385
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2356
The value of delta_label of current 15 th iteration is 0.0011381544388023113 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2427
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2397
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2371
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2344
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2319
delta_label  0.0004377517072316582 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0     2018
1     1599
2     1794
3     1622
4      615
5      451
6      850
7      334
8      282
9      314
10    1009
11     277
12      65
13     120
14      72
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_18"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 15)                480       
=================================================================
Total params: 277,632
Trainable params: 277,632
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.6)is: 15.530126810073853
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne0.6  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.6  into the umap coordinates (adata.obsm)

The run time for all resolution is: 46.4466278553009
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6'
    obsp: 'distances', 'connectivities'
Start to process resolution= 0.8
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.010951042175292969
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 17 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.06907721940115566 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1239
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1028
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0902
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0810
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0738
The value of delta_label of current 2 th iteration is 0.03834704955349326 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1844
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1612
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1450
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1320
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1214
The value of delta_label of current 3 th iteration is 0.03256872701803537 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2178
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1970
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1806
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1675
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1570
The value of delta_label of current 4 th iteration is 0.032481176676589035 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2447
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2256
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2110
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1995
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1903
The value of delta_label of current 5 th iteration is 0.030642619506216075 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2673
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2524
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2408
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2314
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2234
The value of delta_label of current 6 th iteration is 0.0276659078970408 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2821
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2706
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2611
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2530
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2459
The value of delta_label of current 7 th iteration is 0.0224128874102609 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2899
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2804
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2721
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2649
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2584
The value of delta_label of current 8 th iteration is 0.015759061460339695 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2929
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2848
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2775
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2710
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2651
The value of delta_label of current 9 th iteration is 0.011469094729469446 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2927
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2857
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2793
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2737
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2685
The value of delta_label of current 10 th iteration is 0.007091577657152863 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2904
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2845
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2790
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2742
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2696
The value of delta_label of current 11 th iteration is 0.005253020486779898 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2870
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2820
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2772
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2729
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2689
The value of delta_label of current 12 th iteration is 0.0038522150236385924 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2830
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2786
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2744
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2707
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2672
The value of delta_label of current 13 th iteration is 0.0021887585361582912 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2786
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2748
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2711
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2678
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2647
The value of delta_label of current 14 th iteration is 0.0030642619506216075 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2741
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2707
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2675
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2646
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2617
The value of delta_label of current 15 th iteration is 0.0010506040973559797 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2695
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2665
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2637
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2611
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2584
The value of delta_label of current 16 th iteration is 0.0011381544388023113 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2651
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2624
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2599
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2575
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2551
delta_label  0.0004377517072316582 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
0     1545
1     2014
2     1799
3     1387
4      537
5      452
6      951
7      332
8      280
9      310
10    1037
11     278
12     116
13     147
14      57
15      72
16     108
dtype: int64
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_19"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 17)                544       
=================================================================
Total params: 277,696
Trainable params: 277,696
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.8)is: 16.651501178741455
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:28)
computing neighbors
tsne finished and added X_tsne0.8  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.8  into the umap coordinates (adata.obsm)

The run time for all resolution is: 46.80148506164551
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8'
    obsp: 'distances', 'connectivities'
Start to process resolution= 1.0
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.0109710693359375
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 20 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.08220977061810542 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1322
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1118
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0996
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0904
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0829
The value of delta_label of current 2 th iteration is 0.04351251969882682 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1987
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1775
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1613
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1480
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1370
The value of delta_label of current 3 th iteration is 0.031605673262125725 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2377
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2170
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2005
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1873
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1765
The value of delta_label of current 4 th iteration is 0.024251444580633864 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2692
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2503
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2357
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2241
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2146
The value of delta_label of current 5 th iteration is 0.02547714936088251 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2933
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2789
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2674
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2579
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2497
The value of delta_label of current 6 th iteration is 0.022675538434599896 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3086
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2976
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2881
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2801
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2729
The value of delta_label of current 7 th iteration is 0.017334967606373666 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3183
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3090
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3007
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2936
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2870
The value of delta_label of current 8 th iteration is 0.013745403607074068 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3242
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3161
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3086
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3020
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2960
The value of delta_label of current 9 th iteration is 0.01006828926632814 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3271
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3199
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3130
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3070
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3015
The value of delta_label of current 10 th iteration is 0.008930134827525827 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3271
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3208
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3148
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3095
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3045
The value of delta_label of current 11 th iteration is 0.005428121169672562 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3251
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3197
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3144
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3098
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3053
The value of delta_label of current 12 th iteration is 0.004114866047977587 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3220
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3172
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3126
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3084
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3044
The value of delta_label of current 13 th iteration is 0.0037646646821922606 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3182
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3140
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3098
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3060
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3024
The value of delta_label of current 14 th iteration is 0.0021887585361582912 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3140
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3102
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3065
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3030
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2997
The value of delta_label of current 15 th iteration is 0.0014008054631413063 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3095
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3061
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3027
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2996
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2966
delta_label  0.0008755034144633164 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is:
0     1464
1     2037
2     1306
3     1385
4      786
5      451
6      326
7      350
8      332
9      164
10     311
11     664
12    1122
13     245
14     101
15      45
16      72
17     221
18      25
19      15
dtype: int64
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_20"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 20)                640       
=================================================================
Total params: 277,792
Trainable params: 277,792
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=1.0)is: 16.31411623954773
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:28)
computing neighbors
tsne finished and added X_tsne1.0  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.0  into the umap coordinates (adata.obsm)

The run time for all resolution is: 45.77424669265747
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0'
    obsp: 'distances', 'connectivities'
Start to process resolution= 1.2
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.012108087539672852
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 20 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.06811416564524601 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1361
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1145
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1021
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0928
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0852
The value of delta_label of current 2 th iteration is 0.044212922430397476 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2037
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1831
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1666
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1532
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1423
The value of delta_label of current 3 th iteration is 0.03537033794431798 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2417
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2211
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2045
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1914
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1808
The value of delta_label of current 4 th iteration is 0.028016109262826126 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2734
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2542
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2395
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2279
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2186
The value of delta_label of current 5 th iteration is 0.023200840483277883 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2976
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2829
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2714
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2619
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2539
The value of delta_label of current 6 th iteration is 0.021975135703029242 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3125
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3013
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2919
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2838
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2769
The value of delta_label of current 7 th iteration is 0.016809665557695676 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3215
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3123
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3040
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2968
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2905
The value of delta_label of current 8 th iteration is 0.011994396778147435 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3266
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3186
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3111
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3046
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2989
The value of delta_label of current 9 th iteration is 0.009542987217650149 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3285
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3215
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3147
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3089
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3037
The value of delta_label of current 10 th iteration is 0.007616879705830853 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3277
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3217
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3157
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3107
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3060
The value of delta_label of current 11 th iteration is 0.00534057082822623 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3252
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3199
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3148
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3104
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3063
The value of delta_label of current 12 th iteration is 0.0033269129749606023 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3217
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3171
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3126
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3087
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3050
The value of delta_label of current 13 th iteration is 0.003589563999299597 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3178
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3137
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3097
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3061
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3028
The value of delta_label of current 14 th iteration is 0.0015759061460339696 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3135
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3098
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3063
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3030
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3000
The value of delta_label of current 15 th iteration is 0.0011381544388023113 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3090
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3057
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3026
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2995
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2969
The value of delta_label of current 16 th iteration is 0.0010506040973559797 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3044
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3015
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2986
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2958
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2935
delta_label  0.0008755034144633164 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0     1452
1     2039
2     1384
3     1089
4      942
5      782
6      448
7      328
8      353
9      332
10     103
11     314
12    1129
13     242
14     106
15      46
16      72
17     222
18      24
19      15
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_21"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 20)                640       
=================================================================
Total params: 277,792
Trainable params: 277,792
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=1.2)is: 17.398098945617676
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:28)
computing neighbors
tsne finished and added X_tsne1.2  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.2  into the umap coordinates (adata.obsm)

The run time for all resolution is: 46.68986392021179
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2'
    obsp: 'distances', 'connectivities'
Start to process resolution= 1.4
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.011324882507324219
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 22 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.09954473822447908 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1402
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1199
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1083
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0993
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0919
The value of delta_label of current 2 th iteration is 0.04797758711258974 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2085
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1892
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1735
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1603
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1493
The value of delta_label of current 3 th iteration is 0.03510768691997899 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2479
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2275
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2113
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1981
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1874
The value of delta_label of current 4 th iteration is 0.0293293643845211 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2813
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2629
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2485
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2372
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2278
The value of delta_label of current 5 th iteration is 0.02556469970232884 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3055
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2918
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2807
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2717
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2637
The value of delta_label of current 6 th iteration is 0.02311329014183155 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3201
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3096
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3005
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2929
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2858
The value of delta_label of current 7 th iteration is 0.02031167921554894 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3291
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3201
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3119
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3050
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2984
The value of delta_label of current 8 th iteration is 0.01961127648397829 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3345
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3263
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3188
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3123
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3063
The value of delta_label of current 9 th iteration is 0.018823323410961303 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3367
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3294
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3226
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3166
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3111
The value of delta_label of current 10 th iteration is 0.01540886009455437 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3364
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3300
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3239
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3185
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3135
The value of delta_label of current 11 th iteration is 0.017247417264927335 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3342
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3287
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3232
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3183
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3138
The value of delta_label of current 12 th iteration is 0.01444580633864472 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3309
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3260
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3212
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3168
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3127
The value of delta_label of current 13 th iteration is 0.017247417264927335 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3270
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3226
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3183
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3144
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3106
The value of delta_label of current 14 th iteration is 0.018298021362283312 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3226
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3187
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3149
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3113
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3080
The value of delta_label of current 15 th iteration is 0.01286990019261075 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3178
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3144
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3110
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3078
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3047
The value of delta_label of current 16 th iteration is 0.009455436876203817 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3130
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3098
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3068
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3039
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3011
The value of delta_label of current 17 th iteration is 0.006566275608474873 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3082
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3053
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3025
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2998
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2972
The value of delta_label of current 18 th iteration is 0.006040973559796883 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3034
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3008
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2983
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2958
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2935
The value of delta_label of current 19 th iteration is 0.006828926632813868 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2988
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2965
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2943
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2920
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2899
The value of delta_label of current 20 th iteration is 0.005603221852565225 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2945
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2923
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2903
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2883
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2864
The value of delta_label of current 21 th iteration is 0.003677114340745929 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2902
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2883
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2865
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2847
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2829
The value of delta_label of current 22 th iteration is 0.0033269129749606023 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2863
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2845
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2828
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2812
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2796
The value of delta_label of current 23 th iteration is 0.0021887585361582912 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2825
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2809
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2794
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2779
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2765
The value of delta_label of current 24 th iteration is 0.002889161267728944 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2790
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2775
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2762
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2748
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2735
The value of delta_label of current 25 th iteration is 0.003589563999299597 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2757
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2744
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2732
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2719
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2707
The value of delta_label of current 26 th iteration is 0.0038522150236385924 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2727
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2715
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2704
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2692
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2681
The value of delta_label of current 27 th iteration is 0.0023638592190509543 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2699
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2688
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2677
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2667
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2657
The value of delta_label of current 28 th iteration is 0.002714060584836281 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2672
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2662
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2652
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2643
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2633
The value of delta_label of current 29 th iteration is 0.002714060584836281 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2646
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2637
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2628
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2619
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2611
The value of delta_label of current 30 th iteration is 0.002714060584836281 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2622
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2613
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2605
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2597
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2589
The value of delta_label of current 31 th iteration is 0.0019261075118192962 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2599
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2591
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2584
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2576
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2569
The value of delta_label of current 32 th iteration is 0.0018385571703729644 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2578
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2571
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2564
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2557
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2550
The value of delta_label of current 33 th iteration is 0.0014883558045876379 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2558
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2551
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2545
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2538
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2532
The value of delta_label of current 34 th iteration is 0.0033269129749606023 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2540
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2534
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2528
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2522
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2516
The value of delta_label of current 35 th iteration is 0.003151812292067939 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2523
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2517
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2512
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2506
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2500
The value of delta_label of current 36 th iteration is 0.0019261075118192962 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2507
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2502
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2497
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2491
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2486
The value of delta_label of current 37 th iteration is 0.003151812292067939 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2492
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2487
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2482
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2478
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2473
The value of delta_label of current 38 th iteration is 0.003151812292067939 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2478
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2474
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2469
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2465
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2460
The value of delta_label of current 39 th iteration is 0.002889161267728944 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2465
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2461
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2457
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2453
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2449
The value of delta_label of current 40 th iteration is 0.0033269129749606023 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2453
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2449
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2445
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2441
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2437
The value of delta_label of current 41 th iteration is 0.005690772194011557 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2442
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2438
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2434
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2430
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2427
The value of delta_label of current 42 th iteration is 0.006828926632813868 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2431
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2427
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2423
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2420
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2416
The value of delta_label of current 43 th iteration is 0.014008054631413063 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2420
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2417
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2413
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2410
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2407
The value of delta_label of current 44 th iteration is 0.01278234985116442 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2410
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2407
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2404
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2400
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2397
The value of delta_label of current 45 th iteration is 0.02031167921554894 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2400
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2397
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2394
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2391
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2388
The value of delta_label of current 46 th iteration is 0.013220101558396077 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2391
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2388
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2386
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2383
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2380
The value of delta_label of current 47 th iteration is 0.010593591315006128 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2382
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2380
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2377
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2374
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2372
The value of delta_label of current 48 th iteration is 0.010768691997898792 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2374
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2371
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2369
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2366
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2364
The value of delta_label of current 49 th iteration is 0.008404832778847838 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2366
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2364
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2361
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2359
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2356
The value of delta_label of current 50 th iteration is 0.005778322535457888 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2358
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2356
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2353
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2351
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2349
The value of delta_label of current 51 th iteration is 0.0040273157065312554 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2351
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2348
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2346
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2344
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2342
The value of delta_label of current 52 th iteration is 0.0038522150236385924 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2343
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2341
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2339
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2337
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2335
The value of delta_label of current 53 th iteration is 0.001751006828926633 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2336
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2334
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2332
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2330
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2328
delta_label  0.0007879530730169848 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is:
0     1941
1     1381
2     2048
3      980
4        5
5      887
6      763
7      449
8      335
9      355
10     329
11     312
12       2
13     635
14     251
15     109
16      46
17      72
18     221
19     256
20      30
21      15
dtype: int64
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_22"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 22)                704       
=================================================================
Total params: 277,856
Trainable params: 277,856
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=1.4)is: 50.433396100997925
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne1.4  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.4  into the umap coordinates (adata.obsm)

The run time for all resolution is: 80.59438610076904
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4'
    obsp: 'distances', 'connectivities'
Start to process resolution= 1.6
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.01788020133972168
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 23 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.1012957450534057 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1405
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1203
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1087
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0999
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0926
The value of delta_label of current 2 th iteration is 0.04403782174750481 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2089
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1900
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1747
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1618
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1511
The value of delta_label of current 3 th iteration is 0.03361933111539135 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2475
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2280
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2123
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1995
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1891
The value of delta_label of current 4 th iteration is 0.029241814043074767 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2807
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2629
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2490
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2379
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2287
The value of delta_label of current 5 th iteration is 0.026352652775345823 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3055
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2921
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2811
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2722
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2644
The value of delta_label of current 6 th iteration is 0.02285063911749256 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3213
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3109
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3020
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2944
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2875
The value of delta_label of current 7 th iteration is 0.019786377166870952 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3315
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3225
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3145
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3076
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3012
The value of delta_label of current 8 th iteration is 0.021012081947119593 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3383
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3303
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3229
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3164
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3103
The value of delta_label of current 9 th iteration is 0.01768516897215899 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3422
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3349
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3281
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3221
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3166
The value of delta_label of current 10 th iteration is 0.019786377166870952 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3433
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3369
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3308
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3254
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3203
The value of delta_label of current 11 th iteration is 0.021274732971458588 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3424
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3367
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3312
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3262
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3216
The value of delta_label of current 12 th iteration is 0.019961477849763615 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3403
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3352
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3303
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3257
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3215
The value of delta_label of current 13 th iteration is 0.0138329539485204 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3373
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3327
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3283
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3241
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3203
The value of delta_label of current 14 th iteration is 0.010243389949220801 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3337
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3296
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3256
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3217
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3182
The value of delta_label of current 15 th iteration is 0.009805638241989144 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3296
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3258
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3222
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3187
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3154
The value of delta_label of current 16 th iteration is 0.00639117492558221 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3252
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3217
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3185
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3153
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3122
The value of delta_label of current 17 th iteration is 0.005953423218350551 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3206
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3174
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3145
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3116
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3088
The value of delta_label of current 18 th iteration is 0.006040973559796883 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3159
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3131
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3104
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3079
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3054
The value of delta_label of current 19 th iteration is 0.0051654701453335665 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3113
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3088
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3065
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3042
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3020
The value of delta_label of current 20 th iteration is 0.004727718438101909 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3069
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3047
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3026
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3005
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2985
The value of delta_label of current 21 th iteration is 0.003151812292067939 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3028
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3007
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2988
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2969
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2951
The value of delta_label of current 22 th iteration is 0.0032393626335142705 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2988
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2969
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2951
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2934
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2918
The value of delta_label of current 23 th iteration is 0.0023638592190509543 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2950
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2933
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2917
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2901
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2886
The value of delta_label of current 24 th iteration is 0.0032393626335142705 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2915
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2899
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2884
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2870
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2856
The value of delta_label of current 25 th iteration is 0.0023638592190509543 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2881
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2867
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2853
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2840
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2827
The value of delta_label of current 26 th iteration is 0.0015759061460339696 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2849
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2836
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2823
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2811
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2800
The value of delta_label of current 27 th iteration is 0.002714060584836281 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2819
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2807
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2795
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2784
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2774
The value of delta_label of current 28 th iteration is 0.002451409560497286 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2790
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2779
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2769
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2758
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2749
The value of delta_label of current 29 th iteration is 0.0022763088776046225 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2763
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2753
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2743
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2734
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2725
The value of delta_label of current 30 th iteration is 0.003677114340745929 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2738
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2729
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2719
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2710
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2702
The value of delta_label of current 31 th iteration is 0.002889161267728944 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2714
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2705
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2697
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2688
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2681
The value of delta_label of current 32 th iteration is 0.003151812292067939 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2691
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2683
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2675
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2668
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2660
The value of delta_label of current 33 th iteration is 0.004289966730870251 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2670
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2663
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2656
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2648
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2642
The value of delta_label of current 34 th iteration is 0.0032393626335142705 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2650
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2643
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2637
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2630
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2624
The value of delta_label of current 35 th iteration is 0.004202416389423919 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2632
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2625
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2619
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2613
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2607
The value of delta_label of current 36 th iteration is 0.0021887585361582912 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2614
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2609
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2603
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2597
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2591
The value of delta_label of current 37 th iteration is 0.0030642619506216075 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2598
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2592
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2587
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2582
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2576
The value of delta_label of current 38 th iteration is 0.002626510243389949 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2582
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2577
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2572
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2567
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2562
The value of delta_label of current 39 th iteration is 0.004289966730870251 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2567
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2563
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2558
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2553
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2548
The value of delta_label of current 40 th iteration is 0.0032393626335142705 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2554
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2549
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2544
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2540
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2536
The value of delta_label of current 41 th iteration is 0.003151812292067939 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2540
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2536
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2532
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2527
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2523
The value of delta_label of current 42 th iteration is 0.002451409560497286 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2528
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2523
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2519
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2515
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2511
The value of delta_label of current 43 th iteration is 0.003414463316406934 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2515
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2511
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2507
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2504
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2500
The value of delta_label of current 44 th iteration is 0.005603221852565225 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2504
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2500
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2496
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2493
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2489
The value of delta_label of current 45 th iteration is 0.005953423218350551 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2492
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2489
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2486
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2482
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2479
The value of delta_label of current 46 th iteration is 0.008667483803186833 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2482
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2479
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2476
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2472
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2469
The value of delta_label of current 47 th iteration is 0.013132551216949746 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2472
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2469
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2466
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2463
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2461
The value of delta_label of current 48 th iteration is 0.016371913850464017 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2463
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2460
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2458
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2455
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2452
The value of delta_label of current 49 th iteration is 0.021274732971458588 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2455
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2452
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2450
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2447
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2444
The value of delta_label of current 50 th iteration is 0.025389599019436177 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2447
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2444
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2442
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2439
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2437
The value of delta_label of current 51 th iteration is 0.01602171248467869 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2439
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2437
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2435
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2432
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2430
The value of delta_label of current 52 th iteration is 0.007004027315706532 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2432
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2430
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2428
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2425
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2423
The value of delta_label of current 53 th iteration is 0.005253020486779898 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2425
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2423
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2421
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2419
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2417
The value of delta_label of current 54 th iteration is 0.003151812292067939 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2419
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2417
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2415
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2413
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2411
The value of delta_label of current 55 th iteration is 0.0014008054631413063 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2413
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2411
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2409
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2407
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2405
delta_label  0.0 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0     1942
1     1381
2     1984
3      938
4      898
5      769
6      449
7      332
8      654
9      351
10     329
11       1
12     297
13     247
14     109
15      44
16     292
17      72
18     220
19      67
20      31
21      15
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_23"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 23)                736       
=================================================================
Total params: 277,888
Trainable params: 277,888
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=1.6)is: 53.03005409240723
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne1.6  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.6  into the umap coordinates (adata.obsm)

The run time for all resolution is: 83.80500197410583
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6'
    obsp: 'distances', 'connectivities'
Start to process resolution= 1.8
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.012325048446655273
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 23 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.10488530905270531 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1404
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1198
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1080
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0992
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0919
The value of delta_label of current 2 th iteration is 0.04745228506391175 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2081
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1888
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1734
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1607
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1501
The value of delta_label of current 3 th iteration is 0.035983190334442305 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2468
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2273
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2116
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1988
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1883
The value of delta_label of current 4 th iteration is 0.032481176676589035 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2799
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2619
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2479
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2368
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2276
The value of delta_label of current 5 th iteration is 0.02827876028716512 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3045
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2908
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2800
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2710
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2631
The value of delta_label of current 6 th iteration is 0.026615303799684818 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3197
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3093
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3004
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2928
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2858
The value of delta_label of current 7 th iteration is 0.022062686044475574 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3292
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3203
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3124
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3055
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2991
The value of delta_label of current 8 th iteration is 0.02031167921554894 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3351
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3271
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3198
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3134
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3074
The value of delta_label of current 9 th iteration is 0.021099632288565925 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3381
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3309
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3242
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3182
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3127
The value of delta_label of current 10 th iteration is 0.020749430922780598 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3384
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3320
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3260
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3206
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3156
The value of delta_label of current 11 th iteration is 0.023288390824724215 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3370
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3313
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3259
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3211
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3165
The value of delta_label of current 12 th iteration is 0.022675538434599896 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3345
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3294
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3246
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3203
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3160
The value of delta_label of current 13 th iteration is 0.01768516897215899 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3315
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3270
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3226
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3187
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3149
The value of delta_label of current 14 th iteration is 0.013920504289966731 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3281
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3241
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3202
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3167
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3131
The value of delta_label of current 15 th iteration is 0.009980738924881808 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3247
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3210
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3175
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3143
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3110
The value of delta_label of current 16 th iteration is 0.007791980388723516 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3212
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3178
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3146
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3116
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3087
The value of delta_label of current 17 th iteration is 0.007354228681491858 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3176
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3146
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3115
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3088
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3061
The value of delta_label of current 18 th iteration is 0.004552617755209245 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3140
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3112
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3084
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3059
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3033
The value of delta_label of current 19 th iteration is 0.007004027315706532 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3103
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3078
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3053
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3030
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3007
The value of delta_label of current 20 th iteration is 0.004289966730870251 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3066
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3044
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3021
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3000
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2979
The value of delta_label of current 21 th iteration is 0.003414463316406934 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3029
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3009
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2989
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2970
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2951
The value of delta_label of current 22 th iteration is 0.0033269129749606023 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2993
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2975
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2957
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2940
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2922
The value of delta_label of current 23 th iteration is 0.002889161267728944 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2958
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2941
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2925
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2909
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2894
The value of delta_label of current 24 th iteration is 0.0028016109262826126 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2924
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2909
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2894
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2880
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2866
The value of delta_label of current 25 th iteration is 0.0032393626335142705 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2892
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2878
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2864
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2851
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2838
The value of delta_label of current 26 th iteration is 0.0029767116091752757 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2862
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2849
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2836
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2824
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2812
The value of delta_label of current 27 th iteration is 0.002889161267728944 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2832
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2821
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2809
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2798
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2787
The value of delta_label of current 28 th iteration is 0.004114866047977587 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2805
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2794
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2783
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2773
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2763
The value of delta_label of current 29 th iteration is 0.003502013657853266 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2779
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2769
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2759
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2749
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2739
The value of delta_label of current 30 th iteration is 0.002451409560497286 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2754
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2745
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2735
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2726
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2717
The value of delta_label of current 31 th iteration is 0.0032393626335142705 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2730
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2722
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2713
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2705
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2697
The value of delta_label of current 32 th iteration is 0.003414463316406934 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2708
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2700
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2692
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2685
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2677
The value of delta_label of current 33 th iteration is 0.0033269129749606023 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2688
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2680
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2673
Epoch 4/5
45/45 [==============================] - 0s 4ms/step - loss: 0.2666
Epoch 5/5
45/45 [==============================] - 0s 4ms/step - loss: 0.2659
The value of delta_label of current 34 th iteration is 0.00481526877954824 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2668
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2661
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2655
Epoch 4/5
45/45 [==============================] - 0s 4ms/step - loss: 0.2648
Epoch 5/5
45/45 [==============================] - 0s 4ms/step - loss: 0.2641
The value of delta_label of current 35 th iteration is 0.0021887585361582912 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2650
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2644
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2637
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2631
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2625
The value of delta_label of current 36 th iteration is 0.002451409560497286 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2633
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2627
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2621
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2615
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2609
The value of delta_label of current 37 th iteration is 0.0032393626335142705 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2616
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2611
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2605
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2600
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2594
The value of delta_label of current 38 th iteration is 0.0029767116091752757 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2600
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2595
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2590
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2585
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2579
The value of delta_label of current 39 th iteration is 0.0018385571703729644 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2585
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2580
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2575
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2571
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2565
The value of delta_label of current 40 th iteration is 0.0028016109262826126 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2571
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2566
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2561
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2557
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2552
The value of delta_label of current 41 th iteration is 0.00481526877954824 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2557
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2553
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2548
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2544
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2540
The value of delta_label of current 42 th iteration is 0.011031343022237787 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2544
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2540
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2536
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2532
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2528
The value of delta_label of current 43 th iteration is 0.009893188583435476 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2532
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2528
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2524
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2520
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2516
The value of delta_label of current 44 th iteration is 0.015583960777447031 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2520
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2517
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2513
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2509
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2506
The value of delta_label of current 45 th iteration is 0.016722115216249344 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2509
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2506
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2502
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2499
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2495
The value of delta_label of current 46 th iteration is 0.016722115216249344 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2499
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2496
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2492
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2489
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2486
The value of delta_label of current 47 th iteration is 0.014095604972859395 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2489
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2486
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2483
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2480
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2477
The value of delta_label of current 48 th iteration is 0.008930134827525827 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2480
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2477
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2474
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2471
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2468
The value of delta_label of current 49 th iteration is 0.0019261075118192962 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2471
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2468
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2465
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2462
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2459
delta_label  0.0009630537559096481 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0     1947
1     1382
2     2017
3        5
4      976
5      473
6      766
7      448
8      330
9      354
10     331
11     615
12      11
13     295
14     681
15     242
16     101
17      43
18      72
19     220
20      68
21      30
22      15
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_24"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 23)                736       
=================================================================
Total params: 277,888
Trainable params: 277,888
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=1.8)is: 49.09917163848877
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:30)
computing neighbors
tsne finished and added X_tsne1.8  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap1.8  into the umap coordinates (adata.obsm)

The run time for all resolution is: 80.43619990348816
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6', 'desc_1.8'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6', 'prob_matrix1.8'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6', 'X_Embeded_z1.8', 'X_tsne1.8', 'X_umap1.8'
    obsp: 'distances', 'connectivities'
Start to process resolution= 2.0
The number of cpu in your computer is 12
Checking whether result_tmp/ae_weights.h5  exists in the directory
Pretraining time is 0.01738119125366211
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 27 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.13920504289966731 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 1s 3ms/step - loss: 0.1458
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1258
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1147
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1062
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0991
The value of delta_label of current 2 th iteration is 0.06741376291367536 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2176
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1994
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1847
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1725
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1621
The value of delta_label of current 3 th iteration is 0.04964104360007004 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2579
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2399
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2251
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2129
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2027
The value of delta_label of current 4 th iteration is 0.04079845911399054 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2941
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2773
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2640
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2533
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2442
The value of delta_label of current 5 th iteration is 0.0445631237961828 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3222
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3088
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2979
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2889
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2809
The value of delta_label of current 6 th iteration is 0.04920329189283838 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3402
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3295
Epoch 3/5
45/45 [==============================] - 0s 4ms/step - loss: 0.3203
Epoch 4/5
45/45 [==============================] - 0s 4ms/step - loss: 0.3125
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3053
The value of delta_label of current 7 th iteration is 0.04736473472246542 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3512
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3421
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3340
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3269
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3202
The value of delta_label of current 8 th iteration is 0.03256872701803537 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3569
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3489
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3415
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3349
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3287
The value of delta_label of current 9 th iteration is 0.029767116091752758 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3591
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3518
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3451
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3390
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3333
The value of delta_label of current 10 th iteration is 0.02941691472596743 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 4ms/step - loss: 0.3587
Epoch 2/5
45/45 [==============================] - 0s 5ms/step - loss: 0.3524
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3465
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3410
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3358
The value of delta_label of current 11 th iteration is 0.031868324286464716 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3570
Epoch 2/5
45/45 [==============================] - 0s 4ms/step - loss: 0.3516
Epoch 3/5
45/45 [==============================] - 0s 4ms/step - loss: 0.3463
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3414
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3368
The value of delta_label of current 12 th iteration is 0.024776746629311855 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3545
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3497
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3450
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3406
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3365
The value of delta_label of current 13 th iteration is 0.021537383995797584 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3515
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3473
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3430
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3390
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3352
The value of delta_label of current 14 th iteration is 0.015671511118893363 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3480
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3443
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3404
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3368
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3334
The value of delta_label of current 15 th iteration is 0.014270705655752057 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3443
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3409
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3374
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3341
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3310
The value of delta_label of current 16 th iteration is 0.0138329539485204 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3403
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3373
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3340
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3310
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3282
The value of delta_label of current 17 th iteration is 0.013570302924181404 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3362
Epoch 2/5
45/45 [==============================] - 0s 4ms/step - loss: 0.3335
Epoch 3/5
45/45 [==============================] - 0s 4ms/step - loss: 0.3305
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3278
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3252
The value of delta_label of current 18 th iteration is 0.009192785851864822 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3320
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3296
Epoch 3/5
45/45 [==============================] - 0s 4ms/step - loss: 0.3269
Epoch 4/5
45/45 [==============================] - 0s 4ms/step - loss: 0.3244
Epoch 5/5
45/45 [==============================] - 0s 4ms/step - loss: 0.3220
The value of delta_label of current 19 th iteration is 0.010768691997898792 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3280
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3257
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3232
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3210
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3188
The value of delta_label of current 20 th iteration is 0.01006828926632814 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3240
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3219
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3196
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3176
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3155
The value of delta_label of current 21 th iteration is 0.010418490632113465 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3201
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3182
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3161
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3142
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3123
The value of delta_label of current 22 th iteration is 0.008317282437401506 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3164
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3146
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3127
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3109
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3092
The value of delta_label of current 23 th iteration is 0.0074417790229381895 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3128
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3111
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3094
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3077
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3060
The value of delta_label of current 24 th iteration is 0.008667483803186833 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3094
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3078
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3061
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3045
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3030
The value of delta_label of current 25 th iteration is 0.008579933461740501 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3059
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3045
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3029
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3015
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3000
The value of delta_label of current 26 th iteration is 0.006216074242689547 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3026
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.3012
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2998
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2984
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2971
The value of delta_label of current 27 th iteration is 0.005778322535457888 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2994
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2981
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2967
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2955
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2943
The value of delta_label of current 28 th iteration is 0.005953423218350551 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2963
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2951
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2939
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2927
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2916
The value of delta_label of current 29 th iteration is 0.006040973559796883 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2934
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2924
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2912
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2902
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2891
The value of delta_label of current 30 th iteration is 0.006216074242689547 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2908
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2898
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2887
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2877
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2867
The value of delta_label of current 31 th iteration is 0.005778322535457888 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2883
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2873
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2864
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2854
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2845
The value of delta_label of current 32 th iteration is 0.005253020486779898 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2859
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2850
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2841
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2833
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2825
The value of delta_label of current 33 th iteration is 0.004289966730870251 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2837
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2829
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2821
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2813
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2805
The value of delta_label of current 34 th iteration is 0.006040973559796883 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2816
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2808
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2801
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2793
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2786
The value of delta_label of current 35 th iteration is 0.0051654701453335665 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2796
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2789
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2782
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2775
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2769
The value of delta_label of current 36 th iteration is 0.004289966730870251 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2777
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2770
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2764
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2758
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2751
The value of delta_label of current 37 th iteration is 0.004902819120994572 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2759
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2753
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2747
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2741
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2735
The value of delta_label of current 38 th iteration is 0.005077919803887235 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2742
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2736
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2730
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2725
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2719
The value of delta_label of current 39 th iteration is 0.003939765365084924 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2726
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2720
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2714
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2709
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2704
The value of delta_label of current 40 th iteration is 0.006303624584135878 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2710
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2704
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2699
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2694
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2689
The value of delta_label of current 41 th iteration is 0.005778322535457888 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2694
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2689
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2684
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2679
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2674
The value of delta_label of current 42 th iteration is 0.008930134827525827 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2679
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2675
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2670
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2665
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2660
The value of delta_label of current 43 th iteration is 0.01444580633864472 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2665
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2660
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2656
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2651
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2647
The value of delta_label of current 44 th iteration is 0.023726142531955874 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2651
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2647
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2642
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2638
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2634
The value of delta_label of current 45 th iteration is 0.03318157940815969 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2638
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2634
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2630
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2626
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2622
The value of delta_label of current 46 th iteration is 0.039835405358080896 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2626
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2622
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2618
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2614
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2610
The value of delta_label of current 47 th iteration is 0.03239362633514271 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2614
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2610
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2607
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2603
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2599
The value of delta_label of current 48 th iteration is 0.023726142531955874 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2603
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2599
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2596
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2592
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2589
The value of delta_label of current 49 th iteration is 0.00963053755909648 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2592
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2589
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2586
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2582
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2579
The value of delta_label of current 50 th iteration is 0.007879530730169847 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2582
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2579
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2576
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2573
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2570
The value of delta_label of current 51 th iteration is 0.007179127998599194 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2573
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2570
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2567
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2564
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2561
The value of delta_label of current 52 th iteration is 0.00849238312029417 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2564
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2561
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2558
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2555
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2553
The value of delta_label of current 53 th iteration is 0.008755034144633165 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2555
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2552
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2550
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2547
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2545
The value of delta_label of current 54 th iteration is 0.015146209070215374 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2547
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2544
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2542
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2540
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2537
The value of delta_label of current 55 th iteration is 0.016809665557695676 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2539
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2537
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2535
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2532
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2530
The value of delta_label of current 56 th iteration is 0.022500437751707233 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2532
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2530
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2527
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2525
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2523
The value of delta_label of current 57 th iteration is 0.025126947995097182 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2525
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2523
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2520
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2518
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2516
The value of delta_label of current 58 th iteration is 0.02451409560497286 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2518
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2516
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2514
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2512
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2510
The value of delta_label of current 59 th iteration is 0.024776746629311855 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2511
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2509
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2507
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2505
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2503
The value of delta_label of current 60 th iteration is 0.02013657853265628 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2505
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2503
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2501
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2499
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2497
The value of delta_label of current 61 th iteration is 0.019523726142531957 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2499
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2497
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2495
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2493
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2492
The value of delta_label of current 62 th iteration is 0.01812292067939065 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2493
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2491
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2490
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2488
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2486
The value of delta_label of current 63 th iteration is 0.015759061460339695 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2487
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2486
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2484
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2482
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2480
The value of delta_label of current 64 th iteration is 0.014270705655752057 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2482
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2480
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2478
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2477
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2475
The value of delta_label of current 65 th iteration is 0.016371913850464017 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2476
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2475
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2473
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2471
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2470
The value of delta_label of current 66 th iteration is 0.014095604972859395 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2471
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2470
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2468
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2466
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2465
The value of delta_label of current 67 th iteration is 0.01961127648397829 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2466
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2465
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2463
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2461
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2460
The value of delta_label of current 68 th iteration is 0.019348625459639293 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2461
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2460
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2458
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2456
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2455
The value of delta_label of current 69 th iteration is 0.012432148485379093 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2456
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2455
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2453
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2452
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2450
The value of delta_label of current 70 th iteration is 0.009718087900542812 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2452
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2450
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2449
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2447
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2446
The value of delta_label of current 71 th iteration is 0.006566275608474873 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2447
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2445
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2444
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2443
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2441
The value of delta_label of current 72 th iteration is 0.001751006828926633 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2442
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2441
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2440
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2438
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2437
delta_label  0.0001751006828926633 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
The final prediction cluster is:
0     2068
1     1336
2     2140
3      914
4      651
5      761
6      448
7      310
8      365
9      405
10     329
11       1
12     294
13     234
14       2
15     254
16     402
17     183
18      48
19      99
20      21
21      72
22      49
23      21
24      15
dtype: int64
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_25"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 27)                864       
=================================================================
Total params: 278,016
Trainable params: 278,016
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=2.0)is: 70.00197196006775
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:29)
computing neighbors
tsne finished and added X_tsne2.0  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap2.0  into the umap coordinates (adata.obsm)

The run time for all resolution is: 100.4626030921936
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.1', 'desc_0.2', 'desc_0.4', 'desc_0.6', 'desc_0.8', 'desc_1.0', 'desc_1.2', 'desc_1.4', 'desc_1.6', 'desc_1.8', 'desc_2.0'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.1', 'prob_matrix0.2', 'prob_matrix0.4', 'prob_matrix0.6', 'prob_matrix0.8', 'prob_matrix1.0', 'prob_matrix1.2', 'prob_matrix1.4', 'prob_matrix1.6', 'prob_matrix1.8', 'prob_matrix2.0'
    obsm: 'X_Embeded_z0.1', 'X_tsne', 'X_tsne0.1', 'X_umap', 'X_umap0.1', 'X_Embeded_z0.2', 'X_tsne0.2', 'X_umap0.2', 'X_Embeded_z0.4', 'X_tsne0.4', 'X_umap0.4', 'X_Embeded_z0.6', 'X_tsne0.6', 'X_umap0.6', 'X_Embeded_z0.8', 'X_tsne0.8', 'X_umap0.8', 'X_Embeded_z1.0', 'X_tsne1.0', 'X_umap1.0', 'X_Embeded_z1.2', 'X_tsne1.2', 'X_umap1.2', 'X_Embeded_z1.4', 'X_tsne1.4', 'X_umap1.4', 'X_Embeded_z1.6', 'X_tsne1.6', 'X_umap1.6', 'X_Embeded_z1.8', 'X_tsne1.8', 'X_umap1.8', 'X_Embeded_z2.0', 'X_tsne2.0', 'X_umap2.0'
    obsp: 'distances', 'connectivities'
In [45]:
dep_total_clusters
Out[45]:
[8, 9, 11, 15, 17, 20, 20, 22, 22, 23, 25]
In [170]:
#go back and pick a resolution in the middle (0.8) to highlight 
data = desc.train(data, dims=[data.shape[1], 128, 32], tol=0.001, n_neighbors=10,
                   batch_size=256, louvain_resolution=0.8, do_tsne=True, learning_rate=300,
                   do_umap=True, num_Cores_tsne=4)
Start to process resolution= 0.8
The number of cpu in your computer is 12
Create the directory:result_tmp to save result
Checking whether result_tmp/ae_weights.h5  exists in the directory
The file ae_weights.h5 is not exits
Pretraining the 1th layer...
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 1s 7ms/step - loss: 0.4919
Epoch 2/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4660
Epoch 3/50
45/45 [==============================] - 0s 8ms/step - loss: 0.4452
Epoch 4/50
45/45 [==============================] - 0s 8ms/step - loss: 0.4307
Epoch 5/50
45/45 [==============================] - 0s 7ms/step - loss: 0.4200
Epoch 6/50
45/45 [==============================] - 0s 6ms/step - loss: 0.4102
Epoch 7/50
45/45 [==============================] - 0s 6ms/step - loss: 0.4020
Epoch 8/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3955
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3908
Epoch 10/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3872
Epoch 11/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3844
Epoch 12/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3824
Epoch 13/50
45/45 [==============================] - 0s 9ms/step - loss: 0.3805
Epoch 14/50
45/45 [==============================] - 0s 10ms/step - loss: 0.3791
Epoch 15/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3778
Epoch 16/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3767
Epoch 17/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3757
Epoch 18/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3747
Epoch 19/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3740
Epoch 20/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3731
Epoch 21/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3725
Epoch 22/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3717
Epoch 23/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3710
Epoch 24/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3704
Epoch 25/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3697
Epoch 26/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3689
Epoch 27/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3684
Epoch 28/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3678
Epoch 29/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3673
Epoch 30/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3667
Epoch 31/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3663
Epoch 32/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3656
Epoch 33/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3653
Epoch 34/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3648
Epoch 35/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3643
Epoch 36/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3637
Epoch 37/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3634
Epoch 38/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3629
Epoch 39/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3625
Epoch 40/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3621
Epoch 41/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3618
Epoch 42/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3614
Epoch 43/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3611
Epoch 44/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3608
Epoch 45/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3604
Epoch 46/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3600
Epoch 47/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3598
Epoch 48/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3594
Epoch 49/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3592
Epoch 50/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3589
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 2/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3586
Epoch 3/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 4/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 5/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3586
Epoch 6/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 7/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3586
Epoch 8/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3585
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3584
Epoch 11/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3584
Epoch 12/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3583
Epoch 13/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3583
Epoch 14/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3583
Epoch 15/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3582
Epoch 16/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3582
Epoch 17/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3582
Epoch 18/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3582
Epoch 19/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3582
Epoch 20/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3581
Epoch 21/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3582
Epoch 22/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3582
Epoch 23/50
45/45 [==============================] - 0s 7ms/step - loss: 0.3581
Epoch 24/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3581
Epoch 25/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3581
Epoch 26/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 27/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3580
Epoch 28/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 29/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 30/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 31/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 32/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3578
Epoch 33/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 34/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3579
Epoch 35/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3578
Epoch 36/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3577
Epoch 37/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3578
Epoch 38/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3577
Epoch 39/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 40/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 41/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3577
Epoch 42/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 43/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 44/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 45/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3576
Epoch 46/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3575
Epoch 47/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3575
Epoch 48/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
Epoch 49/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
Epoch 50/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3573
Epoch 2/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
Epoch 3/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3573
Epoch 4/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3573
Epoch 5/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3574
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3575
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3574
Epoch 9/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3574
Epoch 10/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3574
Epoch 11/50
45/45 [==============================] - 0s 8ms/step - loss: 0.3574
Epoch 00011: early stopping
The 1th layer has been pretrained.
Pretraining the 2th layer...
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 0s 970us/step - loss: 0.3968
Epoch 2/50
45/45 [==============================] - 0s 890us/step - loss: 0.1693
Epoch 3/50
45/45 [==============================] - 0s 887us/step - loss: 0.1313
Epoch 4/50
45/45 [==============================] - 0s 939us/step - loss: 0.1164
Epoch 5/50
45/45 [==============================] - 0s 923us/step - loss: 0.1076
Epoch 6/50
45/45 [==============================] - 0s 971us/step - loss: 0.1024
Epoch 7/50
45/45 [==============================] - 0s 997us/step - loss: 0.0984
Epoch 8/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0955
Epoch 9/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0932
Epoch 10/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0909
Epoch 11/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0885
Epoch 12/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0866
Epoch 13/50
45/45 [==============================] - 0s 989us/step - loss: 0.0851
Epoch 14/50
45/45 [==============================] - 0s 986us/step - loss: 0.0841
Epoch 15/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0831
Epoch 16/50
45/45 [==============================] - 0s 971us/step - loss: 0.0820
Epoch 17/50
45/45 [==============================] - 0s 967us/step - loss: 0.0814
Epoch 18/50
45/45 [==============================] - 0s 964us/step - loss: 0.0799
Epoch 19/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0800
Epoch 20/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0787
Epoch 21/50
45/45 [==============================] - 0s 953us/step - loss: 0.0781
Epoch 22/50
45/45 [==============================] - 0s 953us/step - loss: 0.0775
Epoch 23/50
45/45 [==============================] - 0s 917us/step - loss: 0.0772
Epoch 24/50
45/45 [==============================] - 0s 933us/step - loss: 0.0766
Epoch 25/50
45/45 [==============================] - 0s 923us/step - loss: 0.0757
Epoch 26/50
45/45 [==============================] - 0s 929us/step - loss: 0.0759
Epoch 27/50
45/45 [==============================] - 0s 956us/step - loss: 0.0750
Epoch 28/50
45/45 [==============================] - 0s 934us/step - loss: 0.0744
Epoch 29/50
45/45 [==============================] - 0s 937us/step - loss: 0.0746
Epoch 30/50
45/45 [==============================] - 0s 914us/step - loss: 0.0733
Epoch 31/50
45/45 [==============================] - 0s 899us/step - loss: 0.0729
Epoch 32/50
45/45 [==============================] - 0s 893us/step - loss: 0.0730
Epoch 33/50
45/45 [==============================] - 0s 905us/step - loss: 0.0727
Epoch 34/50
45/45 [==============================] - 0s 893us/step - loss: 0.0726
Epoch 35/50
45/45 [==============================] - 0s 930us/step - loss: 0.0716
Epoch 36/50
45/45 [==============================] - 0s 957us/step - loss: 0.0716
Epoch 37/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0721
Epoch 38/50
45/45 [==============================] - 0s 983us/step - loss: 0.0709
Epoch 39/50
45/45 [==============================] - 0s 985us/step - loss: 0.0715
Epoch 40/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0706
Epoch 41/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0707
Epoch 42/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0705
Epoch 43/50
45/45 [==============================] - 0s 991us/step - loss: 0.0704
Epoch 44/50
45/45 [==============================] - 0s 972us/step - loss: 0.0696
Epoch 45/50
45/45 [==============================] - 0s 993us/step - loss: 0.0701
Epoch 46/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0697
Epoch 47/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0695
Epoch 48/50
45/45 [==============================] - 0s 984us/step - loss: 0.0697
Epoch 49/50
45/45 [==============================] - 0s 985us/step - loss: 0.0699
Epoch 50/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0691
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0691
Epoch 2/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0689
Epoch 3/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0694
Epoch 4/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0690
Epoch 5/50
45/45 [==============================] - 0s 993us/step - loss: 0.0691
Epoch 6/50
45/45 [==============================] - 0s 928us/step - loss: 0.0689
Epoch 7/50
45/45 [==============================] - 0s 928us/step - loss: 0.0689
Epoch 8/50
45/45 [==============================] - 0s 970us/step - loss: 0.0688
Epoch 9/50
45/45 [==============================] - 0s 964us/step - loss: 0.0688
Epoch 10/50
45/45 [==============================] - 0s 943us/step - loss: 0.0692
Epoch 11/50
45/45 [==============================] - 0s 935us/step - loss: 0.0691
Epoch 12/50
45/45 [==============================] - 0s 921us/step - loss: 0.0688
Epoch 13/50
45/45 [==============================] - 0s 915us/step - loss: 0.0684
Epoch 14/50
45/45 [==============================] - 0s 952us/step - loss: 0.0689
Epoch 15/50
45/45 [==============================] - 0s 930us/step - loss: 0.0690
Epoch 16/50
45/45 [==============================] - 0s 922us/step - loss: 0.0689
Epoch 17/50
45/45 [==============================] - 0s 903us/step - loss: 0.0690
Epoch 18/50
45/45 [==============================] - 0s 901us/step - loss: 0.0687
Epoch 19/50
45/45 [==============================] - 0s 907us/step - loss: 0.0693
Epoch 20/50
45/45 [==============================] - 0s 940us/step - loss: 0.0687
Epoch 21/50
45/45 [==============================] - 0s 941us/step - loss: 0.0688
Epoch 22/50
45/45 [==============================] - 0s 939us/step - loss: 0.0688
Epoch 23/50
45/45 [==============================] - 0s 880us/step - loss: 0.0690
Epoch 00023: early stopping
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0687
Epoch 2/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0686
Epoch 3/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0691
Epoch 4/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0687
Epoch 5/50
45/45 [==============================] - 0s 1ms/step - loss: 0.0688
Epoch 6/50
45/45 [==============================] - 0s 977us/step - loss: 0.0686
Epoch 7/50
45/45 [==============================] - 0s 950us/step - loss: 0.0687
Epoch 8/50
45/45 [==============================] - 0s 933us/step - loss: 0.0686
Epoch 9/50
45/45 [==============================] - 0s 913us/step - loss: 0.0685
Epoch 10/50
45/45 [==============================] - 0s 902us/step - loss: 0.0690
Epoch 11/50
45/45 [==============================] - 0s 916us/step - loss: 0.0688
Epoch 12/50
45/45 [==============================] - 0s 926us/step - loss: 0.0686
Epoch 00012: early stopping
The 2th layer has been pretrained.
Copying layer-wise pretrained weights to deep autoencoders
Fine-tuning autoencoder end-to-end
learning rate = 1
Epoch 1/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3541
Epoch 2/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3525
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3515
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3508
Epoch 5/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3503
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3497
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3492
Epoch 8/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3488
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3483
Epoch 10/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3479
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3475
Epoch 12/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3471
Epoch 13/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3466
Epoch 14/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3462
Epoch 15/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3459
Epoch 16/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3455
Epoch 17/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3451
Epoch 18/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3448
Epoch 19/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3445
Epoch 20/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3441
Epoch 21/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3438
Epoch 22/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3435
Epoch 23/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3432
Epoch 24/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3430
Epoch 25/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3427
Epoch 26/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3425
Epoch 27/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3422
Epoch 28/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3420
Epoch 29/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3417
Epoch 30/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3415
Epoch 31/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3413
Epoch 32/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3411
Epoch 33/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3408
Epoch 34/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3406
Epoch 35/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3404
Epoch 36/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3402
Epoch 37/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3400
Epoch 38/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3398
Epoch 39/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3396
Epoch 40/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3395
Epoch 41/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3393
Epoch 42/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3391
Epoch 43/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3389
Epoch 44/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3388
Epoch 45/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3386
Epoch 46/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3384
Epoch 47/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3383
Epoch 48/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3381
Epoch 49/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3380
Epoch 50/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3378
learning rate = 0.1
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3374
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3373
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3373
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3372
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 12/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 13/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 14/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 15/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 16/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3371
Epoch 17/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 18/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 19/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 20/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 21/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 22/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 23/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 24/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3370
Epoch 25/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 26/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 27/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 28/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 29/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 30/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 31/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3369
Epoch 32/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 33/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 34/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 35/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 36/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 37/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 38/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3368
Epoch 39/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 40/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 41/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 42/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 43/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 44/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 45/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3367
Epoch 46/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3366
Epoch 47/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3366
Epoch 48/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3366
Epoch 49/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3366
Epoch 50/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3366
learning rate = 0.01
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 00011: early stopping
learning rate = 0.001
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 7/50
45/45 [==============================] - 0s 6ms/step - loss: 0.3365
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 00011: early stopping
learning rate = 0.0001
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 00011: early stopping
learning rate = 1e-05
Epoch 1/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 2/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 3/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 4/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 5/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 6/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 7/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 8/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 9/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 10/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 11/50
45/45 [==============================] - 0s 5ms/step - loss: 0.3365
Epoch 00011: early stopping
Pretraining time is 71.79617214202881
Pretrained weights are saved to result_tmp /ae_weights.h5
computing neighbors
...number of clusters is unknown, Initialize cluster centroid using louvain method
    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
running Louvain clustering
    using the "louvain" package of Traag (2017)
    finished: found 17 clusters and added
    'louvain', the cluster labels (adata.obs, categorical) (0:00:01)
The value of delta_label of current 1 th iteration is 0.06907721940115566 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1239
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1028
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0902
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0810
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.0738
The value of delta_label of current 2 th iteration is 0.03834704955349326 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1844
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1612
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1450
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1320
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1214
The value of delta_label of current 3 th iteration is 0.03256872701803537 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2178
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1970
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1806
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1675
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1570
The value of delta_label of current 4 th iteration is 0.032481176676589035 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2447
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2256
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2110
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1995
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.1903
The value of delta_label of current 5 th iteration is 0.030642619506216075 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2673
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2524
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2408
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2314
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2234
The value of delta_label of current 6 th iteration is 0.0276659078970408 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2821
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2706
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2611
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2530
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2459
The value of delta_label of current 7 th iteration is 0.0224128874102609 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2899
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2804
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2721
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2649
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2584
The value of delta_label of current 8 th iteration is 0.015759061460339695 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2929
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2848
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2775
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2710
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2651
The value of delta_label of current 9 th iteration is 0.011469094729469446 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2927
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2857
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2793
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2737
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2685
The value of delta_label of current 10 th iteration is 0.007091577657152863 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2904
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2845
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2790
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2742
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2696
The value of delta_label of current 11 th iteration is 0.005253020486779898 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2870
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2820
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2772
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2729
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2689
The value of delta_label of current 12 th iteration is 0.0038522150236385924 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2830
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2786
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2744
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2707
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2672
The value of delta_label of current 13 th iteration is 0.0021887585361582912 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2786
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2748
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2711
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2678
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2647
The value of delta_label of current 14 th iteration is 0.0030642619506216075 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2741
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2707
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2675
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2646
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2617
The value of delta_label of current 15 th iteration is 0.0010506040973559797 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2695
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2665
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2637
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2611
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2584
The value of delta_label of current 16 th iteration is 0.0011381544388023113 >= tol 0.001
Epoch 1/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2651
Epoch 2/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2624
Epoch 3/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2599
Epoch 4/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2575
Epoch 5/5
45/45 [==============================] - 0s 3ms/step - loss: 0.2551
delta_label  0.0004377517072316582 < tol  0.001
Reached tolerance threshold. Stop training.
WARNING:tensorflow:Compiled the loaded model, but the compiled metrics have yet to be built. `model.compile_metrics` will be empty until you train or evaluate the model.
computing tSNE
WARNING: Consider installing the package MulticoreTSNE (https://github.com/DmitryUlyanov/Multicore-TSNE). Even for n_jobs=1 this speeds up the computation considerably and might yield better converged results.
    using sklearn.manifold.TSNE with a fix by D. DeTomaso
The final prediction cluster is:
0     1545
1     2014
2     1799
3     1387
4      537
5      452
6      951
7      332
8      280
9      310
10    1037
11     278
12     116
13     147
14      57
15      72
16     108
dtype: int64
The desc has been trained successfully!!!!!!
The summary of desc model is:
Model: "model_15"
_________________________________________________________________
Layer (type)                 Output Shape              Param #   
=================================================================
input (InputLayer)           [(None, 2132)]            0         
_________________________________________________________________
encoder_0 (Dense)            (None, 128)               273024    
_________________________________________________________________
encoder_1 (Dense)            (None, 32)                4128      
_________________________________________________________________
clustering (ClusteringLayer) (None, 17)                544       
=================================================================
Total params: 277,696
Trainable params: 277,696
Non-trainable params: 0
_________________________________________________________________
The runtime of (resolution=0.8)is: 88.80368900299072
    finished: added
    'X_tsne', tSNE coordinates (adata.obsm) (0:00:32)
computing neighbors
tsne finished and added X_tsne0.8  into the umap coordinates (adata.obsm)

    finished: added to `.uns['neighbors']`
    `.obsp['distances']`, distances for each pair of neighbors
    `.obsp['connectivities']`, weighted adjacency matrix (0:00:00)
computing UMAP
    finished: added
    'X_umap', UMAP coordinates (adata.obsm) (0:00:00)
umap finished and added X_umap0.8  into the umap coordinates (adata.obsm)

The run time for all resolution is: 122.48604488372803
After training, the information of adata is:
 AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.8'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.8'
    obsm: 'X_Embeded_z0.8', 'X_tsne', 'X_tsne0.8', 'X_umap', 'X_umap0.8'
    obsp: 'distances', 'connectivities'
In [171]:
data
Out[171]:
AnnData object with n_obs × n_vars = 11422 × 2132
    obs: 'n_counts', 'n_genes', 'percent_mito', 'desc_0.8'
    var: 'gene_ids', 'feature_types', 'genome', 'n_cells', 'highly_variable', 'means', 'dispersions', 'dispersions_norm', 'mean', 'std'
    uns: 'log1p', 'hvg', 'umap', 'prob_matrix0.8'
    obsm: 'X_Embeded_z0.8', 'X_tsne', 'X_tsne0.8', 'X_umap', 'X_umap0.8'
    obsp: 'distances', 'connectivities'
In [172]:
prob_1=data.uns["prob_matrix0.8"]
data.obs["max.prob0.8"]=np.max(prob_1,axis=1)
#tSNE plot 
sc.pl.scatter(data,basis="tsne0.8",color=['desc_0.8'])
sc.pl.scatter(data,basis="tsne0.8",color=["max.prob0.8"], legend_fontoutline=5)
In [173]:
from matplotlib.pyplot import rc_context
with rc_context({'figure.figsize': (5, 5)}):
    sc.pl.tsne(data,color=['desc_0.8',"max.prob0.8"], legend_loc='on data',
                  legend_fontsize=10, legend_fontoutline=2,frameon=False, title='scCLEAN', 
               add_outline=True, outline_width=(0.5, 0.05), vmin=0.1,vmax=0.8, ncols=1, 
               save='DESC_Depleted_Res0.8_TSNE_Prrobabilities.png')
    
WARNING: The title list is shorter than the number of panels. Using 'color' value instead for some plots.
WARNING: saving figure to file figures/tsneDESC_Depleted_Res0.8_TSNE_Prrobabilities.png
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